Genome-wide transcriptional responses of two metal-tolerant symbiotic Mesorhizobium isolates to zinc and cadmium exposure
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ABSTRACT:
PROVIDER: PRJNA195616 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR801100.fastq.gz | Fastqsanger.gz | |||
| SRR801101.fastq.gz | Fastqsanger.gz | |||
| SRR801102.fastq.gz | Fastqsanger.gz | |||
| SRR801103.fastq.gz | Fastqsanger.gz | |||
| SRR801104.fastq.gz | Fastqsanger.gz |
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Project description:Mesorhizobium metallidurans STM 2683 and Mesorhizobium sp. strain STM 4661 were isolated from nodules of the metallicolous legume Anthyllis vulneraria from distant mining spoils. They tolerate unusually high zinc and cadmium concentrations as compared to other mesorhizobia. This work aims to study the gene expression profiles associated with zinc or cadmium exposure and to identify genes involved in metal tolerance in these two metallicolous Mesorhizobium strains of interest for mine phytostabilization purposes.
2013-04-02 | GSE45693 | GEO
Project description:Mesorhizobium metallidurans STM 2683 and Mesorhizobium sp. strain STM 4661 were isolated from nodules of the metallicolous legume Anthyllis vulneraria from distant mining spoils. They tolerate unusually high zinc and cadmium concentrations as compared to other mesorhizobia. This work aims to study the gene expression profiles associated with zinc or cadmium exposure and to identify genes involved in metal tolerance in these two metallicolous Mesorhizobium strains of interest for mine phytostabilization purposes. Mesorhizobium metallidurans STM 2683 and Mesorhizobium sp. strain STM 4661 with three treatments (control, Zn and Cd).
2013-04-02 | E-GEOD-45693 | biostudies-arrayexpress
Project description:Mesorhizobium metallidurans STM 2683T and Mesorhizobium sp. strain STM 4661 were isolated from nodules of the metallicolous legume Anthyllis vulneraria from distant mining spoils. They tolerate unusually high Zinc and Cadmium concentrations as compared to other mesorhizobia. This work aims to study the gene expression profiles associated with Zinc or Cadmium exposure and to identify genes involved in metal tolerance in these two metallicolous Mesorhizobium strains of interest for mine phytostabilization purposes.The draft genomes of the two Mezorhizobium strains were sequenced and used to map RNAseq data obtained after Zinc or Cadmium stresses. Comparative genomics and transcriptomics allowed the rapid discovery of metal-specific or/and strain-specific genes. Respectively 1.05% (72/6,844) and 0.97% (68/6,994) predicted Coding DNA Sequences (CDS) for STM 2683 and STM 4661 were significantly differentially expressed upon metal exposure. Among these, a significant number of CDS involved in transport (13/72 and 13/68 for STM 2683 and STM 4661, respectively) and sequestration (15/72 and 16/68 for STM 2683 and STM 4661, respectively) were identified. Thirteen CDS presented homologs in both strains and were differentially regulated by Zinc and/or Cadmium. For instance, several PIB-type ATPases and genes likely to participate in metal sequestration were identified. Among the conserved CDS that showed differential regulation in the two isolates, we also found znuABC homologs encoding for a high affinity ABC-type Zinc import system probably involved in Zinc homeostasis. Additionally, global analyses suggested that both metals also repressed significantly the translational machinery.The comparative RNAseq-based approach revealed a relatively low number of genes significantly regulated in the two Mesorhizobium strains. Very few of them were involved in the non-specific metal response, indicating that the approach was well suited for identifying genes that specifically respond to Zinc and Cadmium. Among significantly up-regulated genes, several encode metal efflux and sequestration systems which can be considered as the most widely represented mechanisms of rhizobial metal tolerance. Downstream functional studies will increase successful phytostabilization strategies by selecting appropriate metallicolous rhizobial partners.
| S-EPMC3668242 | biostudies-literature
Project description:Microarray transcriptomic analysis was carried out on Lotus japonicus plants grown either under purely symbiotic conditions (Mesorhizobium loti) or under non-symbiotic conditions (no inoculation and provided with NH4NO3).
2020-07-02 | E-MTAB-8235 | biostudies-arrayexpress
Project description:Cadmium is an environmental pollutant and significant health hazard that is similar to the physiological metal zinc. In C. elegans high zinc homeostasis is regulated by the HIZR-1 nuclear receptor transcription factor. To define relationships between high zinc homeostasis and the response to cadmium, we identified 145 cadmium-regulated genes. hizr-1 was necessary for activation of a subset of genes, indicating there are at least two mechanisms of cadmium-regulated transcription. Cadmium directly bound HIZR-1, promoted nuclear accumulation of HIZR-1 in intestinal cells, and activated HIZR-1-mediated transcription via the HZA enhancer. Thus, cadmium binding promotes HIZR-1 activity, indicating that cadmium acts as a zinc mimetic to hijack the high zinc response. To elucidate the relationships between high zinc and cadmium detoxification, we analyzed three pathways: the phytochelatin pathway strongly promoted cadmium resistance but not high zinc resistance, the hizr-1 pathway strongly promoted high zinc resistance but not cadmium resistance, and the mek-1/sek-1 pathway promoted resistance to high zinc and cadmium. These studies identify resistance pathways that are specific for high zinc and cadmium as well as a shared pathway.
2021-11-24 | GSE160704 | GEO
Project description:Comparative Genomics of Select Completed Symbiotic Mesorhizobium Genomes
| PRJNA496338 | ENA
Project description:The toxicity of the heavy metal cadmium is well established. However, the molecular basis for how this toxicity perturbs cellular viability is still not well understood. This project investigates the cellular and molecular impacts of cadmium stress in the bacterial pathogen, Streptococcus pneumoniae. We find that cadmium depletes cellular manganese and zinc stores, leading to disruption of metalloproteins and the corresponding biochemical pathways. Furthermore, the over-accumulation of cadmium within the cells appears to facilitate mismetallation events, whereby native metal cofactors are displaced by cadmium, leading to reduced or abrogated enzymatic activity. These metalloproteomic analyses have been conducted in conjunction with transcriptomics and metabolomics to elucidate the global impacts of cadmium stress within a prokaryotic organism.
2021-06-25 | PXD021643 | Pride
Project description:Purpose: Cadmium is a nonessential heavy metal and a well known toxic agent. Cadmium is known to alter the gene expression and signaling but the role of miRNAs during Cadmium exposure is not understood. Methods: Mice were treated with 100 mg/ ml cadmium chloride for 120 days and accumulation of cadmium in blood and organs are confirmed by GFAAS. Subsequently, the total RNA was isolated from the whole blood and small RNA sequencing was executed in Illumina HiSeq 1000. Results: The reads were annotated to the mice genome and miRNAs in miRbase using miRDeep* and novel miRNAs were also predicted. The differential expression was studied by DeSeq Conclusions: This is the first report to reveal the cadmium responsive miRNome. These candidate miRNAs can serve as biomarkers for cadmium
2015-11-01 | GSE73744 | GEO
Project description:Exposure to cadmium is associated with a variety of human diseases. At low concentrations, cadmium activates the transcription of stress-responsive genes, which can prevent or repair the adverse effects caused by this metal. Using C. elegans, 290 genes were identified that are differentially expressed (≥1.5-fold) following a 4 or 24 hour exposure to cadmium. Several of these genes are known to be involved in metal detoxification, including mtl-1, mtl-2, cdr-1 and ttm-1, confirming the efficacy of the study. The majority, however, were not previously associated with metal-responsiveness and are novel. Gene Ontology analysis mapped these genes to cellular/ion trafficking, metabolic enzymes and proteolysis categories. RNAi-mediated inhibition of 50 cadmium-responsive genes resulted in an increased sensitivity to cadmium toxicity, demonstrating that these genes are involved in the resistance to cadmium toxicity. Several functional protein interacting networks were identified by interactome analysis. Within one network, the signaling protein KEL-8 was identified. Kel-8 protects C. elegans from cadmium toxicity in a mek-1 (MAPKK)-dependent manner. Because many C. elegans genes and signal transduction pathways are evolutionarily conserved, these results may contribute to the understanding of the functional roles of various genes in cadmium toxicity in higher organisms. Keywords: gene expression time course
2008-03-26 | GSE7535 | GEO
Project description:Purpose: Cadmium is a nonessential heavy metal and a well known toxic agent. Cadmium is known to alter the gene expression and signaling but the role of miRNAs during Cadmium exposure is not understood. Methods: Mice were treated with 100 mg/ ml cadmium chloride for 120 days and accumulation of cadmium in blood and organs are confirmed by GFAAS. Subsequently, the total RNA was isolated from the whole blood and small RNA sequencing was executed in Illumina HiSeq 1000. Results: The reads were annotated to the mice genome and miRNAs in miRbase using miRDeep* and novel miRNAs were also predicted. The differential expression was studied by DeSeq Conclusions: This is the first report to reveal the cadmium responsive miRNome. These candidate miRNAs can serve as biomarkers for cadmium Whole blood small RNA profiles of control and cadmium exposed mice generated by deep sequencing using Illumina HiSeq 1000
2015-11-01 | E-GEOD-73744 | biostudies-arrayexpress