Gene expression of Tetrahymena thermophila SB210 under the arsenic exposure
Ontology highlight
ABSTRACT:
ORGANISM(S): Tetrahymena thermophila Tetrahymena thermophila SB210
PROVIDER: GSE53836 | GEO | 2019/12/01
REPOSITORIES: GEO
Similar Datasets
Project description:Five genome-wide microarrays were used to indentify gene expression in exposure to Tributyltin, Dichlorodiphenyltrichloroethane and 2, 3, 7, 8-Tetrachlorodibenzo-p-dioxin. The three environmental chemicals are persistent in environment and cause continuous toxical effects on human and aquatic life. Tetrahymena thermophila has the potential as a toxical model. The genome-wide microarray in Tetrahymena thermophila exposed to these toxicants was analyzed. First, genes differentially expressed under the treatment of each toxicant were identified and then their functions were categorized using GO enrichment analysis. The results may suggest that Tetrahymena thermophila is able to reflect different mechanism of different toxic-type toxicants which are similar to those in multicellular organisms. Regarding the complexity of TCDD effects, context likelihood of relatedness method (CLR) was applied to construct a TCDD-relevant network. General functions of the network are related to the epigenetic mechanism of TCDD. Based on the network analysis, a model of TCDD effect on T. thermophila was infered. Thus, Tetrahymena has the potential to be a good unicellular eukaryotic model for toxic mechanism research at genome level. Tetrahymena thermophila CU428 cells were cultured using 1XSPP, 30 degree, 100 rpm shaking, until 300,000 cells/ml. Cells at 300,000 cells/ml was incubated in SPP medium were treated. Two microarrays were used 4.02μl DMSO per ml SPP as the solvent and control; One microarray for 5 ppb TBT treatment 24 hours; One microarray for 1 ppb TCDD treatment 24 hours; One microarray for 4ppm DDT treatment for 24 hours.
2011-06-30 | E-GEOD-26515 | biostudies-arrayexpress
Project description:Five genome-wide microarrays were used to indentify gene expression in exposure to Tributyltin, Dichlorodiphenyltrichloroethane and 2, 3, 7, 8-Tetrachlorodibenzo-p-dioxin. The three environmental chemicals are persistent in environment and cause continuous toxical effects on human and aquatic life. Tetrahymena thermophila has the potential as a toxical model. The genome-wide microarray in Tetrahymena thermophila exposed to these toxicants was analyzed. First, genes differentially expressed under the treatment of each toxicant were identified and then their functions were categorized using GO enrichment analysis. The results may suggest that Tetrahymena thermophila is able to reflect different mechanism of different toxic-type toxicants which are similar to those in multicellular organisms. Regarding the complexity of TCDD effects, context likelihood of relatedness method (CLR) was applied to construct a TCDD-relevant network. General functions of the network are related to the epigenetic mechanism of TCDD. Based on the network analysis, a model of TCDD effect on T. thermophila was infered. Thus, Tetrahymena has the potential to be a good unicellular eukaryotic model for toxic mechanism research at genome level.
2011-06-30 | GSE26515 | GEO
Project description:Arsenic is known as a human carcinogen that easily be exposed by the living organisms through environment and food consumption. The arsenic is transport into the cells via phosphate transporters due to its structural similarity with phosphate in both prokaryotes and eukaryotes. We here evaluated and analyzed the toxicogenomic impacts of arsenate and the role of different phosphate concentrations on arsenic toxicity. Our results showed that arsenic uncoupled phosphate levels which eventually affected the growth rate of yeast cells. Analysis of arsenate levels in the medium over 4 to 10 h of its exposure clearly showed that arsenate was easily taken up by the cells in phosphate limited condition.
2009-12-31 | GSE14991 | GEO
Project description:In endolysosomal networks, two hetero-hexameric tethers called HOPS and CORVET are found widely throughout eukaryotes. The ciliate Tetrahymena thermophila is a unicellular organism with elaborate endolysosomal pathways. Curiously, Tetrahymena and related protozoa have lost HOPS. Tetrahymena encodes multiple paralogs of most CORVET subunits, assembled into six distinct hexameric complexes, including a distinct Vps8 subunit. Here we analyze the composition of these complexes immunoisolated by affinity capture using the Vps8-FLAG paralogs as bait.
2019-12-19 | PXD014895 | Pride
Project description:Stress constantly challenges plant adaptation to the environment. Of all stress types, arsenic was a major threat during the early evolution of plants. The most prevalent chemical form of arsenic is arsenate, whose similarity to phosphate renders it easily incorporated into cells via the phosphate transporters. Here we found that arsenate stress provokes a notable transposon burst in plants, in coordination with arsenate/phosphate transporter repression, which immediately restricts arsenate uptake. This repression was accompanied by delocalization of the phosphate transporter from the plasma membrane. When arsenate was removed, the system rapidly restored transcriptional expression and membrane localization of the transporter. We identify WRKY6 as an arsenate-responsive transcription factor that mediates arsenate/phosphate transporter gene expression and restricts arsenate-induced transposon activation. Plants therefore have a dual WRKY-dependent signaling mechanism that modulates arsenate uptake and transposon expression, providing a coordinated strategy for arsenate tolerance and transposon gene silencing.
2014-04-25 | GSE49037 | GEO
Project description:Stress constantly challenges plant adaptation to the environment. Of all stress types, arsenic was a major threat during the early evolution of plants. The most prevalent chemical form of arsenic is arsenate, whose similarity to phosphate renders it easily incorporated into cells via the phosphate transporters. Here we found that arsenate stress provokes a notable transposon burst in plants, in coordination with arsenate/phosphate transporter repression, which immediately restricts arsenate uptake. This repression was accompanied by delocalization of the phosphate transporter from the plasma membrane. When arsenate was removed, the system rapidly restored transcriptional expression and membrane localization of the transporter. We identify WRKY6 as an arsenate-responsive transcription factor that mediates arsenate/phosphate transporter gene expression and restricts arsenate-induced transposon activation. Plants therefore have a dual WRKY-dependent signaling mechanism that modulates arsenate uptake and transposon expression, providing a coordinated strategy for arsenate tolerance and transposon gene silencing. Three biological replicates were performed for each sample type. Single channel hybridizations were carried-out using either Affymetrix ATH1 platform or Nimblegen Gene Expression 12x135K platform (Arabidopsis thaliana).
2014-04-25 | E-GEOD-49037 | biostudies-arrayexpress
Project description:ABSTRACT: Inorganic arsenic is a carcinogen and its ingestion in foods such as rice presents a significant risk to human health. Plants chemically reduce arsenate to arsenite. Using genome-wide association (GWA) mapping of loci controlling natural variation in arsenic accumulation in Arabidopsis thaliana allowed us to identify the arsenate reductase required for this reduction, which we named High Arsenic Content1 (HAC1). Complementation verified the identity of HAC1, and expression in Escherichia coli lacking a functional arsenate reductase confirmed the arsenate reductase activity of HAC1. The HAC1 protein accumulates in the epidermis, the outer cell layer of the root, and also in the pericycle cells surrounding the central vascular tissue. Plants lacking HAC1 lose their ability to efflux arsenite from roots, leading to both increased transport of arsenic into the central vascular tissue and on into the shoot. HAC1 therefore functions to reduce arsenate to arsenite in the outer cell layer of the root, facilitating efflux of arsenic as arsenite back into the soil to limit its accumulation in the root and transport to the shoot. Arsenate reduction by HAC1 in the pericycle may play a role in limiting arsenic loading into the xylem. Loss of HAC1 encoded arsenic reduction leads to a significant increase in arsenic accumulation in shoots causing an increased sensitivity to arsenate toxicity. We also confirmed the previous observation that the ACR2 arsenate reductase in A. thaliana plays no detectable role in arsenic metabolism. Further, ACR2 does not interact epistatically with HAC1, since arsenic metabolism in the acr2 hac1 double mutant is disrupted in an identical manner to that described for the hac1 single mutant. Our identification of HAC1 and its associated natural variation provides an important new resource for the development of low arsenic containing food stuffs such as rice.
2014-10-15 | GSE62299 | GEO
Project description:ABSTRACT: Inorganic arsenic is a carcinogen and its ingestion in foods such as rice presents a significant risk to human health. Plants chemically reduce arsenate to arsenite. Using genome-wide association (GWA) mapping of loci controlling natural variation in arsenic accumulation in Arabidopsis thaliana allowed us to identify the arsenate reductase required for this reduction, which we named High Arsenic Content1 (HAC1). Complementation verified the identity of HAC1, and expression in Escherichia coli lacking a functional arsenate reductase confirmed the arsenate reductase activity of HAC1. The HAC1 protein accumulates in the epidermis, the outer cell layer of the root, and also in the pericycle cells surrounding the central vascular tissue. Plants lacking HAC1 lose their ability to efflux arsenite from roots, leading to both increased transport of arsenic into the central vascular tissue and on into the shoot. HAC1 therefore functions to reduce arsenate to arsenite in the outer cell layer of the root, facilitating efflux of arsenic as arsenite back into the soil to limit its accumulation in the root and transport to the shoot. Arsenate reduction by HAC1 in the pericycle may play a role in limiting arsenic loading into the xylem. Loss of HAC1 encoded arsenic reduction leads to a significant increase in arsenic accumulation in shoots causing an increased sensitivity to arsenate toxicity. We also confirmed the previous observation that the ACR2 arsenate reductase in A. thaliana plays no detectable role in arsenic metabolism. Further, ACR2 does not interact epistatically with HAC1, since arsenic metabolism in the acr2 hac1 double mutant is disrupted in an identical manner to that described for the hac1 single mutant. Our identification of HAC1 and its associated natural variation provides an important new resource for the development of low arsenic containing food stuffs such as rice. Hybridizations from a set of Bulk Segregant analysis. We measured the elemental profile of 315 F2 plants from a cross between the high arsenic Arabidopsis thaliana accession Kr-0 and the the low arsenic accession Col-0, data available at www.ionomicshub.org <http://www.ionomicshub.org>. Leaves from the 59 highest and 61 lowest arsenic 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.
2014-10-15 | E-GEOD-62299 | biostudies-arrayexpress
Project description:We present a comprehensive transcriptome of ciliate T. thermophila using the Illumina RNA-seq platform. The data was generated from the six mRNA samples of growth, starvation and conjugation of Tetrahymena. Despite an AT rich genome, there are about 124.6 million reads mapped to T. thermophila genome. Using these mapped reads, we have significantly improved the previous genome annotation and investigated the gene expression. Besides, our result also provided a comprehensive understanding of the alternative splicing in T. thermophila, and suggested the existence of the regulated unproductive splicing and translation (RUST) in the single-celled eukaryote. RNA-seq for six samples of Tetrahymena growth, starvation and conjugation.
2012-03-15 | E-GEOD-27971 | biostudies-arrayexpress
Project description:In most eukaryotes, the meiotic chromosomal bouquet (comprising clustered chromosome ends) provides an ordered chromosome arrangement that facilitates pairing and recombination between homologous chromosomes. In the protist Tetrahymena thermophila, the meiotic prophase nucleus stretches enormously and chromosomes assume a bouquet-like arrangement in which telomeres and centromeres are attached to opposite poles of the nucleus. We have identified and characterized three meiosis-specific genes (MELG1-3) that control nuclear elongation and centromere and telomere clustering. Hence, to find out potential interactions, we did LC-MS/MS analysis for Melg1, Melg2, Melg3, and Tass1 (a partner of Melg3) immunoprecipitation samples.
2020-11-23 | PXD021813 | Pride