Expression data from arabidopsis root in response to boron toxicity
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE32659 | GEO | 2011/11/01
SECONDARY ACCESSION(S): PRJNA147057
REPOSITORIES: GEO
Similar Datasets
Project description:Boron is an essential micronutrient for plants and is taken up in the form of boric acid (BA). Despite this, a high BA concentration is toxic for the plants, inhibiting root growth and is thus a significant problem in semi-arid areas in the world. In this work, we report the molecular basis for the inhibition of root growth caused by boron. We used microarrays to detail the global gene expression underlying boron toxicity in roots. 5-day-old arabidopsis plants were transferred to medium with high boron concentration (½ MS medium supplemented with 5mM BA) and control conditions (½ MS medium). We determined that 5 mM BA is the minimum concentration that produces the maximum effect, stunting root growth by ~50% after 5 days as compared with control conditions. We analyzed the transcript profiles in roots by microarray analysis (Affymetrix ATH1 Genome Array). We compared the transcripts obtained at 12 hrs of BA treatment.
2011-11-01 | E-GEOD-32659 | biostudies-arrayexpress
Project description:Poplars are known to be highly tolerant species to boron toxicity and accumulation. However, genes and molecular networks responsible in boron toxicity tolerance have not been investigated yet. Therefore, we performed a pot experiment with 20 black poplar clones collected from the vicinity of boron mines and polluted areas to investigate its potential role in phytoremediation and to select the most boron toxicity tolerant genotype. Trees were treated with irrigation water containing seven elevated boron concentrations from 0 to 160 ppm. Then a microarray based comparative transcriptome profiling was conducted to identify boron toxicity regulated genes responsible in defence responses of black poplar. The results of the study indicated that black poplar is quite suitable for phytoremediation of boron pollution. It could resist 15 ppm soil B content and < 1600 mg/kg boron accumulation in leaves which are highly toxic concentrations for almost all agricultural plants. Transcriptomics results of study revealed totally 1625 and 1419 altered probe sets under boron toxicity in leaf and root tissues, respectively. The highest induction were recorded for the probes sets annotated to tyrosine aminotransferase, ATP binding cassette transporters, glutathione S transferases and metallochaperone proteins. Strong up regulation of these genes attributed to internal excretion of boron into the cell vacuole and existence of detoxification processes in black poplar. Many candidate genes functional in signalling, gene regulation, antioxidation, boron uptake, transport and detoxification processes were also identified in the current study. This is the first transcriptomic study identifying boron toxicity regulated poplar genes and their potential role in boron toxicity tolerance.
2016-06-28 | GSE83745 | GEO
Project description:Poplars are known to be highly tolerant species to boron toxicity and accumulation. However, genes and molecular networks responsible in boron toxicity tolerance have not been investigated yet. Therefore, we performed a pot experiment with 20 black poplar clones collected from the vicinity of boron mines and polluted areas to investigate its potential role in phytoremediation and to select the most boron toxicity tolerant genotype. Trees were treated with irrigation water containing seven elevated boron concentrations from 0 to 160 ppm. Then a microarray based comparative transcriptome profiling was conducted to identify boron toxicity regulated genes responsible in defence responses of black poplar. The results of the study indicated that black poplar is quite suitable for phytoremediation of boron pollution. It could resist 15 ppm soil B content and < 1600 mg/kg boron accumulation in leaves which are highly toxic concentrations for almost all agricultural plants. Transcriptomics results of study revealed totally 1625 and 1419 altered probe sets under boron toxicity in leaf and root tissues, respectively. The highest induction were recorded for the probes sets annotated to tyrosine aminotransferase, ATP binding cassette transporters, glutathione S transferases and metallochaperone proteins. Strong up regulation of these genes attributed to internal excretion of boron into the cell vacuole and existence of detoxification processes in black poplar. Many candidate genes functional in signalling, gene regulation, antioxidation, boron uptake, transport and detoxification processes were also identified in the current study. This is the first transcriptomic study identifying boron toxicity regulated poplar genes and their potential role in boron toxicity tolerance. Total RNA used in microarray experiment was isolated from the leaves and roots of black poplar clone; N.92.237 which accumulated the highest amount of boron its tissues. Total RNA used in the microarray experiment was isolated from leaves and roots of three black poplar saplings grown in ~ 2 ppm (control) and ~ 15 ppm (toxic) soil B contents. RNA isolation was made according to Lithium chloride precipitation method described in Chang et al. (1993). These three isolated RNAs (biological replicates) for each tissue loaded onto three Affymetrix poplar Gene Chips (technical replicates). Totally, 12 GeneChips (2 tissues Ã? 2 different B treatment Ã? 3 biological replicates) were used for transcriptional analysis.
2016-06-28 | E-GEOD-83745 | biostudies-arrayexpress
Project description:Boron (B) is an essential micronutrient for vascular plants. Boron works to build the cell wall structure by forming borate ester cross-links with pectin, and the deficiency of this element brings about oxidative damage and cell death. However, the process via which B deficiency leads to such serious damage has not been well understood. We investigated the temporal changes in metabolism of B-deprived cultured tobacco (Nicotiana tabacum) BY-2 cells by analyzing their gene expression using cDNA microarray.
2012-05-05 | GSE37649 | GEO
Project description:Boron is essential for plants, and boron availability in soil is an important determinant of agricultural production. Boron availability in soil is limited at many regions in the world, including Japan. Under boron deficient conditions, leaf expansion and root elongation, apical dominance, flower development,and fruit and seed sets are inhibited. In this work, we analyzed the mRNA expression of genes containing AUGUAA motif in their 5′-UTR, which is induced by boron. We used microarrays to detail the global gene expression underlying boron deficiency in roots.
2013-11-13 | GSE52208 | GEO
Project description:One of the essential or beneficial micronutrient for plants and animals is boron that is an ultra-trace element. Although boron can inhibit the growth of Saccharomyces cerevisiae around 80 mM, it is also a growth supplement. However, little information is currently available regarding the molecular mechanisms and essentiality of boron. In this paper, the approach was to generate S. cerevisiae mutants with high boron resistance by using evolutionary engineering strategy that was previously applied successfully. Boron-resistant S. cerevisiae mutants were obtained and their phenotypic and physiological characteristics were determined. In order to identify the molecular mechanisms implicated in boron resistance, the whole transcriptomes and genome sequence analysis of wild type and one of the most resistant mutants were compared.
2023-02-07 | GSE224764 | GEO
Project description:Boron is essential for plants, and boron availability in soil is an important determinant of agricultural production. Boron availability in soil is limited at many regions in the world, including Japan. Under boron deficient conditions, leaf expansion and root elongation, apical dominance, flower development,and fruit and seed sets are inhibited. In this work, we analyzed the mRNA expression of genes containing AUGUAA motif in their 5M-bM-^@M-2-UTR, which is induced by boron. We used microarrays to detail the global gene expression underlying boron deficiency in roots. Plants were grown on solid medium containing 1% (w/v) sucrose, 1.5% (w/v) gellan gum and 100 M-BM-5M boron for 10 days and then transferred to 0.3 and 100 M-BM-5M boron for 2 days. Plates were placed vertically at 22M-BM-0C in a growth chamber under long-day conditions (16 h light/8 h dark cycle). We analyzed the transcript profiles in roots by microarray analysis (Affymetrix ATH1 Genome Array).
2013-11-13 | E-GEOD-52208 | biostudies-arrayexpress
Project description:Boron (B) is an essential nutrient for normal growth of plants. Despite its low abundance in soils, B pollution and toxicity have been reported to increase in especially arid and semi-arid environments. Poplars are known to be tolerant species to B toxicity and accumulation. In the current study, physiological, transcriptomic and hormonal regulations behind B toxicity response were investigated comparatively in poplar species. Previously identified clones of Populus nigra (P.n) and Populus alba (P.a) having contrasting B accumulation and leaf B toxicity symptoms were treated with elevated soil B supply in a pot trial. The physiological results of treatment indicated better biomass growth, higher leaf chlorophyll content and more than three folds lower B accumulation in leaves of P.a compared to P.n. Microarray based transcriptomic analysis revealed 1902 and 1006 differentially regulated transcripts for the leaves and roots of P.a, respectively. Several transcripts responsible in salicylic acid (SA) production (salicylic acid binding protein 2) and SA dependent gene regulation (chitinases, proteases, lipases and protease inhibitors) were strongly upregulated specifically in P.a tissues under B toxicity. Furthermore, endogenous SA content in the roots and leaves of P.a increased with a soil B concentration-dependent manner while there was no significant alteration in the same hormone for P.n tissues under B toxicity. Therefore, increase in endogenous SA concentration was strongly attributed to lower B uptake and B toxicity tolerance in P.a. In addition to SA mediated gene regulation, genes responsible in external excretion process was also supposed to be functional in P.a for reduction of tissue B content under toxic conditions. On the other hand, transcriptome profiling of P.n under B toxicity revealed 1624 and 1419 altered transcripts for the leaves and roots, respectively. Specific induction in transcripts annotated to ATP binding cassette B type transporters, glutathione S transferases and metallochaperones in P.n were linked to internal excretion of excess B in the species that could be related with much higher B uptake from the roots, directional transport to the leaves and detoxification under toxic B conditions.
2018-04-01 | GSE97335 | GEO
Project description:Barley1 GeneChip was used to investigate transcriptome changes associated with boron (B) toxicity in a sensitive barley cultivar (Hordeum vulgare L. cv. Hamidiye). Eight day old aseptically grown seedlings were subjected to 5 or 10 mM boric acid (B(OH)3) treatments for 5 days and expression profiles were determined with DNA microarrays using total RNA from leaf tissues. Surface sterilized seeds were aseptically germinated and grown on half strength Hoaglandâs solution (Hoagland and Arnon, 1950) (pH 5.8) solidified with Phytagel® for 8 days at 23±2ºC with 16 h light (400 µmol mâ2 sâ1) and 8 h dark photo-cycle with 70% relative humidity. Seedlings were transferred to sterile hydroponic cultures for B treatment, which was applied immediately after transfer as half strength Hoaglandâs solution containing either 5 mM B(OH)3 (5B) or 10 mM B(OH)3 (10B) for another 5 days under the same physical conditions. Control (C) groups were transferred to half strength Hoaglandâs solution without extra B(OH)3. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Mehmet Tufan OZ. The equivalent experiment is BB63 at PLEXdb.] Experiment Overall Design: treated or untreated: Control (C)(3-replications); treated or untreated: 5 mM B(OH)3 treatment (5B)(3-replications); treated or untreated: 10 mM B(OH)3 treatment (10B)(3-replications)
2009-01-31 | E-GEOD-14521 | biostudies-arrayexpress
Project description:Here we report, that levels of the micronutrient boron are instrumental for meristem maintenance by integration into specific meristem maintenance pathways. We used RNA-seq analysis of the boron deficient maize mutant tassel-less1 to identify early molecular defects induced by boron deficiency in maize reproductive (tassel) meristems. RNA-seq results were independently verified through downstream in silico, double mutant, microscopy, proteomic, and molecular analyses.
2022-08-31 | GSE169600 | GEO