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Transcriptomic analysis of a nickel-resistant Saccharomyces cerevisiae mutant obtained by evolutionary engineering

ABSTRACT: Nickel-resistant Saccharomyces cerevisiae mutant was obtained by evolutionary engineering. The reference strain which was used to select this nickel-resistant mutant could not grow even at 0.5 mM NiCl2 whereas this mutant was shown to be resistant upto 5.3 mM NiCl2 concentration. Whole-genome microarray analysis might be promising to identify the nickel resistance mechanisms in the yeast cells. The reference Saccharomyces cerevisiae strain and the nickel-resistant mutant were grown in minimal medium to an Optical Density (OD600) of 1.00 which correspond to the logarithmic growth phase of the yeast cells. Cultures were harvested and whole RNA isolation was carried out. The experiment was repeated three times.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: CEREN ALKIM

PROVIDER: E-GEOD-50985 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptomic analysis of a nickel-resistant Saccharomyces cerevisiae mutant obtained by evolutionary engineering

Project description:Nickel-resistant Saccharomyces cerevisiae mutant was obtained by evolutionary engineering. The reference strain which was used to select this nickel-resistant mutant could not grow even at 0.5 mM NiCl2 whereas this mutant was shown to be resistant upto 5.3 mM NiCl2 concentration. Whole-genome microarray analysis might be promising to identify the nickel resistance mechanisms in the yeast cells.

2013-09-19 | GSE50985 | GEO

Transcriptomic analysis of an iron-resistant Saccharomyces cerevisiae mutant obtained by evolutionary engineering

Project description:Iron-resistant Saccharomyces cerevisiae mutant was obtained by evolutionary engineering selection strategy. The mutant obtained M-bM-^@M-^\M8FEM-bM-^@M-^] is much more resistant to iron stress than the reference strain which was used to select this mutant. Mutant can resist up to 35mM Iron* stress whereas the reference strain cannot. Whole-genome microarray analysis might be promising to identify the iron resistance mechanisms and stress response upon high levels of iron in the yeast cells. Iron-resistant mutant is also cross resistant to Cobalt, Chromium and Nickel but sensitive to Zinc. * refers to [NH4]2[Fe][SO4]2 and FeCl2. The reference Saccharomyces cerevisiae strain and the iron-resistant mutant were grown in minimal medium to an Optical Density (OD600) of 1.00 which correspond to the logarithmic growth phase of the yeast cells. Cultures were harvested and whole RNA isolation was carried out. The experiment was repeated three times.

2014-09-11 | E-GEOD-61317 | biostudies-arrayexpress

Transcriptomic analysis of a NaCl-resistant Saccharomyces cerevisiae mutant obtained by evolutionary engineering

Project description:NaCl-resistant Saccharomyces cerevisiae mutant was obtained by evolutionary engineering. EMS mutagenized culture was used as the initial population for the selection procedure. Gradually increasing levels of NaCl stress was applied through 40 successive batch cultivations. The reference strain could not grow even at 0.85 M NaCl whereas this mutant was shown to be resistant up to 1.45 M NaCl concentration. Whole-genome microarray analysis was used to identify the NaCl resistance mechanisms by comparing NaCl-resistant mutant strain and the reference strain in the absence of NaCl stress. The reference Saccharomyces cerevisiae strain and the NaCl-resistant mutant were grown in minimal medium to an Optical Density (OD600) of 1.00 which corresponds to the logarithmic growth phase of the yeast cells. Cultures were harvested and whole RNA isolation was carried out. The experiment was repeated three times.

2014-09-30 | E-GEOD-61903 | biostudies-arrayexpress

Evolutionary Engineering and Transcriptomic Analysis of Phenylethanol-resistant Saccharomyces cerevisiae

Project description:Phenylethanol-resistant S. cerevisiae mutants were obtained by using evolutionary engineering strategy. Briefly, a chemically mutagenized culture was used as the initial population for the selection procedure. Gradually increasing levels of phenylethanol stress was applied through 56 successive batch cultivations. Individual mutants were selected from the final population. The mutant with the highest phenylethanol resistance could resist up to 3 g/L phenylethanol concentrations. Whole-genome transcriptomic analyses of the phenylethanol-resistant mutant strain and the reference strain were performed by using DNA microarray technology, in the absence of phenylethanol stress. Agilent yeast DNA microarray systems were used for whole-genome transcriptomic analyses of the reference strain and the selected phenylethanol-resistant mutant. Three replicates of each culture were grown in 100 mL yeast minimal medium using 500 mL flasks, at 30Â°C and 150 rpm. Cells at logarithmic phase of growth (~1.0 OD600) were used for total RNA isolation.

2014-07-12 | E-GEOD-59353 | biostudies-arrayexpress

Transcriptomics data on E. coli lacking queuosine tRNA modification (tgt deficient strain) exposed or not to nickel stress.

Project description:Purpose: to observe differences in E. coli transcripts levels due to the absence of the tRNA modification queuosine and due to exposure to excess nickel. Methods: RNAseq was performed using the total RNA isolated from E. coli MG1655 WT and Δtgt strains grown in LB medium only or in LB added by 2 mM NiCl2. Results: in nickel-treated WT compared to untreated WT (WT_Ni/WT_LB) 734 genes were found up-regulated and 1,642 genes down-regulated in the treated cells; in the tgt mutant compared to the WT strain (tgt_LB/WT_LB), 417 genes were found up regulated and 1,053 genes down regulated in the tgt mutant. Conclusions: the gene expression pattern of the tgt deficient cell in LB medium resembles the one of the WT strain exposed to nickel, showing repression of iron-import genes and genes associated to anaerobic metabolism; increased resistance to nickel stress observed in the tgt mutant is explained by the repression of the nickel import system nikABCCDE.

2022-05-15 | GSE181239 | GEO

Transcriptomic analysis of two ethanol-tolerant Saccharomyces cerevisiae clones obtained by evolutionary engineering

Project description:Evolutionary engineering strategy was used for selection of ethanol-tolerant Saccharomyces cerevisiae clones under gradually increasing ethanol stress levels. Clones B2 and B8 were selected based on their higher ethanol-tolerance and higher ethanol production levels. Whole genome microarray analysis was used for identifying the gene expression levels of these two evolved clones compared to the reference strain. Two evolved ethanol-tolerant strains B2 and B8, which were selected by evolutionary engineering under gradually increasing ethanol stress, were used for whole genome transcriptomic analysis in comparison with the reference strain. Cells were grown in yeast minimal media until they reach a final OD600 of 1. Following total RNA isolation, gene expression levels were analyzed using One-color microarray-based gene expression analysis (Agilent Technologies). Experiments were done in triplicates.

2016-03-01 | E-GEOD-78759 | biostudies-arrayexpress

Mechanisms of nickel toxicity in bacteria

Project description:We report the effects of a nickel stress on the transcriptome of Escherichia coli coli cells, evaluated by RNA-Seq experiments Comparison between wild type E. coli grown in miminal media in the presence or not of 50 ÂµM NiCl2 during 10 min - 2 conditions compared with 3 replicates each

2016-07-01 | E-GEOD-76167 | biostudies-arrayexpress

Epigenetic Repogramming by an Environmental Carcinogen Through Chromatin Domain Disruption [ChIP-Seq]

Project description:Alterations in chromatin modifications, including DNA methylation and histone modification patterns, have been characterized under exposure of several environmental pollutants, including nickel. As with other carcinogenic metals, the mutagenic potential of nickel compounds is low and is not well correlated with its carcinogenic effects. Nickel exposure, however, is associated with alterations in chromatin modifications and related transcriptional programs, suggesting an alternative pathway whereby nickel exposure can lead to disease. To investigate the extent to which nickel exposure disrupts chromatin patterns, we profiled several histone modifications, including H3K4me3, H3K9ac, H3K27me3 and H3K9me2 as well as the insulator binding protein CTCF and the transcriptomes of control BEAS-2B cells and cells treated with nickel for 72 hours. Our results show significant alterations of the repressive histone modification H3K9me2 in nickel-exposed cells with spreading of H3K9me2 into new domains associated with gene silencing. We furthermore show that local regions of active chromatin can protect genes from nickel-induced H3K9me2 spreading. Interestingly, we show that nickel exposure selectively disrupts weaker CTCF sites, leading to spreading of H3K9me2 at these regions. These results have major implications in the understanding of how environmental carcinogens can affect chromatin dynamics and the consequences of chromatin domain disruption in disease progression. Treat BEAS-2B cells with NiCl2 for 72 hours and compare histone modification, CTCF binding to control BEAS-2B cells to see how they regulated gene expression by RNA-seq

2014-09-26 | E-GEOD-56051 | biostudies-arrayexpress

Epigenetic Repogramming by an Environmental Carcinogen Through Chromatin Domain Disruption [RNA-Seq]

2014-09-26 | E-GEOD-56052 | biostudies-arrayexpress

Nickel Chloride (NiCl2) effect on human T cells from whole blood

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. We obtained mRNA of purified human CD3+ T cells from 3 different donors that were treated with or without 1000 μM nickel chloride for 1 h and then stimulated with anti-CD3/anti-CD28 for 6 h.

2011-05-18 | E-GEOD-23387 | biostudies-arrayexpress

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