Ontology highlight
ABSTRACT:
PROVIDER: PRJNA994147 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25249200_1.fastq.gz | Fastqsanger.gz | |||
| SRR25249200_2.fastq.gz | Fastqsanger.gz | |||
| SRR25249201_1.fastq.gz | Fastqsanger.gz | |||
| SRR25249201_2.fastq.gz | Fastqsanger.gz | |||
| SRR25249202_1.fastq.gz | Fastqsanger.gz |
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Project description:Cells that have been pre-exposed to mild stress (priming stress) acquire transient resistance to subsequent severe stress even under different combinations of stresses. This phenomenon is called cross-tolerance. Although it has been reported that cross-tolerance occurs in many organisms, the molecular basis is not clear yet. Here, we identified slm9+ as a responsible gene for the cross-tolerance in the fission yeast Schizosaccharomyces pombe. Slm9 is a homolog of mammalian HIRA histone chaperone. HIRA forms a conserved complex and gene disruption of other HIRA complex components, Hip1, Hip3, and Hip4, also yielded a cross-tolerance-defective phenotype, indicating that the fission yeast HIRA is involved in the cross-tolerance as a complex. We also revealed that Slm9 was recruited to the stress-responsive gene loci upon stress treatment in an Atf1-dependent manner. The expression of stress-responsive genes under stress conditions was compromised in HIRA disruptants. Consistent with this, Pol II recruitment and nucleosome eviction at these gene loci were impaired in slm9D cells. Furthermore, we found that the priming stress enhanced the expression of stress-responsive genes in wild-type cells that were exposed to the severe stress. These observations suggest that HIRA functions in stress response through transcriptional regulation. To determine whether fission yeast HIRA specifically regulates stress-responsive genes under stress condition, we performed genome-wide analysis by using Affymetrix GeneChip oligonucleotide microarrays.
2012-07-22 | GSE35281 | GEO
Project description:7 transition metals (silver, arsenic, cadmium, chromium, copper, mercury and zinc) were treated (2hr) on diploid yeast BY4743. Keywords: Response to metals
2008-11-01 | GSE9466 | GEO
Project description:Cells that have been pre-exposed to mild stress (priming stress) acquire transient resistance to subsequent severe stress even under different combinations of stresses. This phenomenon is called cross-tolerance. Although it has been reported that cross-tolerance occurs in many organisms, the molecular basis is not clear yet. Here, we identified slm9+ as a responsible gene for the cross-tolerance in the fission yeast Schizosaccharomyces pombe. Slm9 is a homolog of mammalian HIRA histone chaperone. HIRA forms a conserved complex and gene disruption of other HIRA complex components, Hip1, Hip3, and Hip4, also yielded a cross-tolerance-defective phenotype, indicating that the fission yeast HIRA is involved in the cross-tolerance as a complex. We also revealed that Slm9 was recruited to the stress-responsive gene loci upon stress treatment in an Atf1-dependent manner. The expression of stress-responsive genes under stress conditions was compromised in HIRA disruptants. Consistent with this, Pol II recruitment and nucleosome eviction at these gene loci were impaired in slm9D cells. Furthermore, we found that the priming stress enhanced the expression of stress-responsive genes in wild-type cells that were exposed to the severe stress. These observations suggest that HIRA functions in stress response through transcriptional regulation. To determine whether fission yeast HIRA specifically regulates stress-responsive genes under stress condition, we performed genome-wide analysis by using Affymetrix GeneChip oligonucleotide microarrays. Fission yeast cells (WT, slm9D, hip1D) were grown in quadruplicate at 32°C to the logarithmic phase and an aliquot was collected as the unstressed control. The other three aliquots were exposed to 40°C for 1 h, 25 mM H2O2 for 1 h, or 40°C for 1 h followed by 25 mM H2O2 for 1 h, respectively. Total RNA was purified and all the 12 RNA samples were analyzed with GeneChip Yeast Genome 2.0 Array (Affymetrix).
2012-07-21 | E-GEOD-35281 | biostudies-arrayexpress
Project description:Background: The high number of heavy metal resistance genes in the soil bacterium Cupriavidus metallidurans CH34 makes it an interesting model organism to study microbial responses to heavy metals. Results: In this study the transcriptional response of this bacterium was measured after challenging it to a wide range of sub-lethal concentrations of various essential or toxic metals. Considering the global transcriptional responses for each challenge as well as by identifying the overlap in upregulated genes between different metal responses, the sixteen metals could be clustered in three different groups. Additionally, next to the assessment of the transcriptional response of already known metal resistance genes, new metal response gene clusters were identified. The majority of the metal response loci showed similar expression profiles when cells were exposed to different metals, suggesting complex cross-talk at transcriptional level between the different metal responses. The highly redundant nature of these metal resistant regions – illustrated by the large number of paralogous genes – combined with the phylogenetic distribution of these metal response regions within evolutionary related and other metal resistant bacteria, provides important insights on the recent evolution of this naturally soil dwelling bacterium towards a highly metal-resistant strain found in harsh and anthropogenic environments. Conclusions: The metal-resistant soil bacterium Cupriavidus metallidurans CH34 displays myriads of gene expression patterns when exposed to a wide range of heavy metals at non-lethal concentrations. The interplay between the different gene expression clusters points towards a complex cross-regulated regulatory network governing heavy metal resistance in C. metallidurans CH34. Keywords: Cupriavidus metallidurans CH34, transcriptional regulation, heavy metal resistance Two-condition experiments. Comparing samples after induction with heavy metals versus non-induced samples. Biological duplicate or triplicate. Each array contains 3 or 4 technical replicates.
2011-06-28 | E-GEOD-23876 | biostudies-arrayexpress
Project description:Background: The high number of heavy metal resistance genes in the soil bacterium Cupriavidus metallidurans CH34 makes it an interesting model organism to study microbial responses to heavy metals. Results: In this study the transcriptional response of this bacterium was measured after challenging it to a wide range of sub-lethal concentrations of various essential or toxic metals. Considering the global transcriptional responses for each challenge as well as by identifying the overlap in upregulated genes between different metal responses, the sixteen metals could be clustered in three different groups. Additionally, next to the assessment of the transcriptional response of already known metal resistance genes, new metal response gene clusters were identified. The majority of the metal response loci showed similar expression profiles when cells were exposed to different metals, suggesting complex cross-talk at transcriptional level between the different metal responses. The highly redundant nature of these metal resistant regions – illustrated by the large number of paralogous genes – combined with the phylogenetic distribution of these metal response regions within evolutionary related and other metal resistant bacteria, provides important insights on the recent evolution of this naturally soil dwelling bacterium towards a highly metal-resistant strain found in harsh and anthropogenic environments. Conclusions: The metal-resistant soil bacterium Cupriavidus metallidurans CH34 displays myriads of gene expression patterns when exposed to a wide range of heavy metals at non-lethal concentrations. The interplay between the different gene expression clusters points towards a complex cross-regulated regulatory network governing heavy metal resistance in C. metallidurans CH34. Keywords: Cupriavidus metallidurans CH34, transcriptional regulation, heavy metal resistance
2011-06-28 | GSE23876 | GEO
Project description:Candida albicansis a commensal yeast that has important impacts on host metabolism and immune function, and can establish life-threatening infections in immunocompromised individuals. Previously,C. albicanscolonization has been shown to contribute to the progression and severity of alcoholic liver disease. However, relatively little is known about howC. albicansresponds to changing environmental conditions in the GI tract of individuals with alcohol use disorder, namely repeated exposure to ethanol. In this study, we repeatedly exposedC. albicansto high concentrations (10% vol/vol) of ethanol—a concentration that can be observed in the upper GI tract of humans following consumption of alcohol. Following this repeated exposure protocol, ethanol small colony (Esc) variants ofC. albicansisolated from these populations exhibited increased ethanol tolerance, altered transcriptional responses to ethanol, and cross-resistance/tolerance to the frontline antifungal fluconazole. These Esc strains exhibited chromosomal copy number variations and carried polymorphisms in genes previously associated with the acquisition of fluconazole resistance during human infection. This study identifies a selective pressure that can result in evolution of fluconazole tolerance and resistance without previous exposure to the drug.
2024-02-28 | GSE243757 | GEO
Project description:Plants growing in soil are challenged by multiple biotic (e.g. pathogens) and abiotic (e.g. heavy metals) stressors. Stress resistance is a key determinant for plants to thrive in the environment. Resistance to pathogens requires innate immunity , whereas tolerance to metal ions is accomplished by mechanisms such as complexation and compartmentation. Some transition metals can enhance plant’s defense against pathogens4,5, but the mechanism remains unclear. Here, we show that an Arabidopsis head-to-head gene pair of intracellular nucleotide-binding leucine-rich repeat (NLR) receptors antagonistically control transition metal-triggered immunity. One NLR, STM2 directly perceives transition metal ions, such as Cd2+, Cu2+ and Zn2+, as a ligand to activate its NAD+ hydrolytic activity and immune responses, triggering enhanced resistance to the soil-borne bacterial wilt pathogen Ralstonia solanacearum. The other NLR, STM1 suppresses STM2 to protect plants from transition metal-triggered immunity and growth inhibition in the presence of excess metals. STM1 also dampens resistance to the pathogen. Our study defines an NLR activated by transition metals and reveals a trade-off between resistance to pathogens and tolerance to transition metals that are pervasive in soil.
2025-03-11 | GSE291226 | GEO
Project description:Plants growing in soil are challenged by multiple biotic (e.g. pathogens) and abiotic (e.g. heavy metals) stressors. Stress resistance is a key determinant for plants to thrive in the environment. Resistance to pathogens requires innate immunity 1, whereas tolerance to metal ions is accomplished by mechanisms such as complexation and compartmentation2,3. Some transition metals can enhance plant’s defense against pathogens4,5, but the mechanism remains unclear. Here, we show that an Arabidopsis head-to-head gene pair of intracellular nucleotide-binding leucine-rich repeat (NLR) receptors antagonistically control transition metal-triggered immunity. One NLR, STM2 directly perceives transition metal ions, such as Cd2+, Cu2+ and Zn2+, as a ligand to activate its NAD+ hydrolytic activity and immune responses, triggering enhanced resistance to the soil-borne bacterial wilt pathogen Ralstonia solanacearum. The other NLR, STM1 suppresses STM2 to protect plants from transition metal-triggered immunity and growth inhibition in the presence of excess metals. STM1 also dampens resistance to the pathogen. Our study defines an NLR activated by transition metals and reveals a trade-off between resistance to pathogens and tolerance to transition metals that are pervasive in soil.
2025-03-10 | GSE291114 | GEO