Ontology highlight
ABSTRACT:
PROVIDER: PRJNA798731 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17664700.fastq.gz | Fastqsanger.gz | |||
| SRR17664701.fastq.gz | Fastqsanger.gz | |||
| SRR17664702.fastq.gz | Fastqsanger.gz | |||
| SRR17664703.fastq.gz | Fastqsanger.gz | |||
| SRR17664704.fastq.gz | Fastqsanger.gz |
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Project description:To identify the transcriptional targets of the DNA-binding response regulator HnoC (SO_2540), mRNA transcript levels in Shewanella oneidensis were measured using whole genome microarray analysis. Transcript levels were compared between WT Shewanella oneidensis and a hnoC deletion strain.
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Project description:To identify the transcriptional targets of the DNA-binding response regulator HnoC (SO_2540), mRNA transcript levels in Shewanella oneidensis were measured using whole genome microarray analysis. Transcript levels were compared between WT Shewanella oneidensis and a hnoC deletion strain. Transcript levels of a WT and hnoC deletion strain were measured after 15 hrs growth, 4 independent replicates were performed for each strain
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Project description:The ionizing radiation (IR) dose that yields 20% survival (D20) of Shewanella oneidensis MR-1 is lower by factors of 20 and 200 than for Escherichia coli and Deinococcus radiodurans, respectively. Transcriptome analysis was used to identify the genes of MR-1 responding to 40 Gy (D20). We observed the induction of 170 genes and repression of 87 genes in MR-1 during a one-hour recovery period after irradiation. The genomic response of MR-1 to IR is very similar to its response to ultraviolet radiation (254 nm), which included induction of systems involved in DNA repair and prophage synthesis, and the absence of differential regulation of tricarboxylic acid cycle activity which occurs in IR-irradiated D. radiodurans. Furthermore, strong induction of genes encoding antioxidant enzymes in MR-1 was observed. DNA damage may not be the principal cause of high sensitivity to IR considering that MR-1 encodes a complex set of DNA repair systems and 40 Gy IR induces less than one double strand break (DSB) in its genome. Instead, a combination of oxidative stress, protein damage and prophage mediated cell lysis during irradiation and recovery might underlie this organism’s great sensitivity to radiation. Keywords: time course, stress response
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Project description:The availability of oxygen is a major environmental factor for many microbes, in particular for bacteria, such as Shewanella species, which thrive in redox-stratified environments. One of the best studied systems involved in mediating the response to changes in environmental oxygen levels is the Arc two-component system of Escherichia coli, consisting of the sensor kinase ArcB and the cognate response regulator ArcA. An ArcA ortholog was previously identified in Shewanella, and as in E. coli, Shewanella ArcA is involved in regulating the response to shifts in oxygen levels. Here, we identified the hybrid sensor kinase SO_0577, now designated ArcS, as the previously elusive cognate sensor kinase of the Arc system in S. oneidensis MR-1. Phenotypic mutant characterization, transcriptomic analysis, protein-protein interaction and phosphotransfer studies revealed that the Shewanella Arc system consists of the sensor kinase ArcS, the single phosphotransfer domain protein HptA, and the response regulator ArcA. Phylogenetic analysis suggests that HptA might be a relict of ArcB. Conversely, ArcS is substantially different with respect to overall sequence homologies and domain organization. Thus, we speculate ArcS might have adopted the role of ArcB after loss of the original sensor kinase, perhaps as a consequence of regulatory adaptation to a redox-stratified environment. In the study presented, expression profiles of three independent replicates of Shewanella oneidensis MR-1 delta-arcS were compared to three independent replicates of Shewanella oneidensis MR-1 wild type cells. All samples were obtained from exponentially aerobically grown cells in LB
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Project description:Comparison of gene expression and mutant fitness in Shewanella oneidensis MR-1
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