Ontology highlight
ABSTRACT:
PROVIDER: PRJNA657949 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12474064.fastq.gz | Fastqsanger.gz |
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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: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:For environmental safety, the high concentration of heavy metals in the soil should be removed. Cadmium (Cd), one of the heavy metals polluting the soil while its concentration exceeds 3.4 mg/kg in soil. Potential use of cotton for remediating heavy Cd-polluted soils is available while its molecular mechanisms of Cd tolerance remains unclear in cotton. In this study, transcriptome analysis was used to identify the Cd tolerance genes and their potential mechanism in cotton. Finally 4,627 differentially expressed genes (DEGs) in the root, 3,022 DEGs in the stem and 3,854 DEGs in leaves were identified through RNA-Seq analysis, respectively. These genes contained heavy metal transporter genes (ABC, CDF, HMA, etc.), annexin genes, heat shock genes (HSP) amongst others. Gene ontology (GO) analysis showed that the DEGs were mainly involved in the oxidation-reduction process and metal ion binding. The DEGs mainly enriched in two pathways, the influenza A and the pyruvate pathway. GhHMAD5 protein, containing a heavy-metal domain, was identified in the pathway to transport or to detoxify the heavy ion. GhHMAD5-overexpressed plants of Arabidopsis thaliana showed the longer roots compared with the control. Meanwhile, GhHMAD5-silenced cotton plants showed more sensitive to Cd stress compared with the control. The results indicated that GhHMAD5 gene is remarkably involved in Cd tolerance, which gives us a preliminary understanding of Cd tolerance mechanisms in upland cotton. Overall, this study provides valuable information for the use of cotton to remediate the soil polluted with heavy metals.
2019-04-25 | GSE126671 | GEO