Expression data from Aracidopsis roots
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE118293 | GEO | 2019/08/01
REPOSITORIES: GEO
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Project description:Plants utilize soil sulfate for production of sulfur-containing amino acids that serve as essential dietary sulfur sources for animals. Despite the global nutritional significance of this fundamental metabolic process in nature, transcription factors regulating the plant sulfur assimilation pathways have never been discovered. We isolated sulfur limitation1 (slim1) mutants from Arabidopsis, showing abnormally low expression of SULTR1;2 sulfate transporter, by screening responsiveness of SULTR1;2 promoter-GFP, as an indicator, to sulfur limitation. SLIM1 encoded an EIL-family transcription factor, EIL3. To clarify the siganificance of SLIM1 function in sulfur responsive gene expression, we analyzed the transcriptome profiles in slim1-1, slim1-2 and the parental line under +S and -S conditions. Keywords: comparison of mutant and wild type, sulfur limitation response, nutritional stress response
2006-12-19 | GSE4455 | GEO
Project description:Plants utilize soil sulfate for production of sulfur-containing amino acids that serve as essential dietary sulfur sources for animals. Despite the global nutritional significance of this fundamental metabolic process in nature, transcription factors regulating the plant sulfur assimilation pathways have never been discovered. We isolated sulfur limitation1 (slim1) mutants from Arabidopsis, showing abnormally low expression of SULTR1;2 sulfate transporter, by screening responsiveness of SULTR1;2 promoter-GFP, as an indicator, to sulfur limitation. SLIM1 encoded an EIL-family transcription factor, EIL3. To clarify the siganificance of SLIM1 function in sulfur responsive gene expression, we analyzed the transcriptome profiles in slim1-1, slim1-2 and the parental line under +S and -S conditions. Experiment Overall Design: PSULTR1;2-GFP, slim1-1 and slim1-2 were vertically grown on the +S/-S (S1500/S15) agar medium. Root tissues of 10-day-old plants were used for RNA extraction and hybridization on Affymetrix microarrays. All conditions were duplicated.
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2017-08-16 | GSE93048 | GEO
Project description:ABSTRACT: Natural variation allows the investigation of both the fundamental functions of genes and their role in local adaptation. As one of the essential macronutrients, sulfur is vital for plant growth and development, and also for crop yield and quality. Selenium and sulfur are assimilated by the same process, and although plants do not require selenium, plant-based selenium is an important source of this essential element for animals. Here, we report the use of linkage mapping in synthetic F2 populations, and complementation to investigate the genetic architecture of variation in total leaf sulfur and selenium concentrations in a diverse set of Arabidopsis thaliana accessions. We identify in accessions collected from Sweden and the Czech Republic two variants of the enzyme adenosine 5-phosphosulfate reductase 2 (APR2) with strongly diminished catalytic capacity. APR2 is a key enzyme in both sulfate and selenate reduction and its reduced activity in the loss-of-function allele apr2-1 and the two A. thaliana accessions Hodon¨ªn (Hod) and Shahdara (Sha), leads to a lowering of sulfur flux from sulfate into the reduced sulfur compounds, cysteine and glutathione, and into proteins, concomitant with an increase in the accumulation of sulfate in leaves. We conclude from our observation, and the previously identified weak allele of APR2 from the Sha accession collected in Tadjikistan, that the catalytic capacity of APR2 varies by four orders of magnitude across the A. thaliana species range, driving significant differences in sulfur and selenium metabolism. The selective benefit, if any, of this large variation remains to be explored.
2014-10-01 | GSE61922 | GEO
Project description:ABSTRACT: Natural variation allows the investigation of both the fundamental functions of genes and their role in local adaptation. As one of the essential macronutrients, sulfur is vital for plant growth and development, and also for crop yield and quality. Selenium and sulfur are assimilated by the same process, and although plants do not require selenium, plant-based selenium is an important source of this essential element for animals. Here, we report the use of linkage mapping in synthetic F2 populations, and complementation to investigate the genetic architecture of variation in total leaf sulfur and selenium concentrations in a diverse set of Arabidopsis thaliana accessions. We identify in accessions collected from Sweden and the Czech Republic two variants of the enzyme adenosine 5-phosphosulfate reductase 2 (APR2) with strongly diminished catalytic capacity. APR2 is a key enzyme in both sulfate and selenate reduction and its reduced activity in the loss-of-function allele apr2-1 and the two A. thaliana accessions Hodon¨ªn (Hod) and Shahdara (Sha), leads to a lowering of sulfur flux from sulfate into the reduced sulfur compounds, cysteine and glutathione, and into proteins, concomitant with an increase in the accumulation of sulfate in leaves. We conclude from our observation, and the previously identified weak allele of APR2 from the Sha accession collected in Tadjikistan, that the catalytic capacity of APR2 varies by four orders of magnitude across the A. thaliana species range, driving significant differences in sulfur and selenium metabolism. The selective benefit, if any, of this large variation remains to be explored. genomic hybridization bulked segregant analysis Hybridizations from a set of Bulk Segregant analysis. We measured the elemental profile of 328 F2 plants from a cross between the high sulfur and selenium Arabidopsis thaliana accession Hod and the Col-0 accession, data available at www.ionomicshub.org <http://www.ionomicshub.org>). Leaves from the 57 highest and 61 lowest sulfur and selenium accumulating plants (calculated as a percentage of the Col-0 accumulation in the same growth tray) were pooled and the genomic DNA was extracted using Qiagen kits.
2014-10-01 | E-GEOD-61922 | biostudies-arrayexpress
Project description:Gene expression in response to changes in sulfur supply was studied in P. aeruginosa E601, a cystic fibrosis isolate that displays mucin sulfatase activity, and in P. aeruginosa PAO1. A large family of genes was found to be upregulated by sulfate limitation in both isolates, encoding sulfatases and sulfonatases, transport systems, oxidative stress proteins, and a sulfate-regulated TonB/ExbBD complex. These genes were localized in five distinct islands on the genome, and encoded proteins with a significantly reduced content of cysteine and methionine. Growth of P. aeruginosa E601 with mucin as sulfur source led to a sulfate starvation response, but also to induction of genes involved with type III secretion systems. Experiment Overall Design: Gene expression in exponential-phase cells was analysed using Affymetrix arrays. Sulfur was supplied either as sulfate, or as the non-sulfate S sources cyclamate (sodium cyclohexylsulfamate) and mucin (human colon cell line mucin LS174T). Control experiments were also done with combinations of these sulfur sources. Studies with mucin as sulfur source were carried out with P. aeruginosa E601 (a CF isolate with mucin sulfatase activity) and comparative studies were performed with P. aeruginosa PAO1. Experiments with strain E601 were done in 3-4 fold replication, experiments with strain PAO1 with 2-3 fold replication.
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Project description:Competition among nitrate reducing bacteria (NRB) and sulfate reducing bacteria (SRB) for resources in anoxic environments is generally thought to be governed largely by thermodynamics. It is now recognized that intermediates of nitrogen and sulfur cycling (e.g., hydrogen sulfide, nitrite, etc.) can also directly impact NRB and SRB activities in freshwater, wastewater and sediment, and therefore may play important roles in competitive interactions. Here, using Intrasporangium calvum C5 as a model NRB, we performed comparative transcriptomic and metabolomic analyses to demonstrate that the reduced sulfur compounds cysteine and sulfide differentially inhibit respiratory growth on nitrate, and that inhibition by each can be selectively relieved by a specific carbon source. These findings provide mechanistic insights into the interplay and stratification of NRBs and SRBs in diverse environments.
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