Escherichia coli K-12: 0%, 10% and 30% hydrogen peroxide (H2O2) treatments, in wild type and luxS mutants
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ABSTRACT:
ORGANISM(S): Escherichia coli
SUBMITTER: Aram Kang
PROVIDER: E-GEOD-38186 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Transcriptional profiling of Escherichia coli K-12 comparing luxS mutant LW12 with wild type W3110 exposure to 10mM or 30mM hydrogen peroxide. Two-condition experiment, luxS mutant LW12 vs. wild type W3110, treatment with 10mM hydrogen peroxide for 30min or treatment with 30mM hydrogen peroxide for 30min. Two biological replicates.
2014-05-08 | E-GEOD-16335 | biostudies-arrayexpress
Project description:Transcripitonal profiling of Escherichia coli K-12 comparing luxS mutant LW12 with wild type W3110 One-condition experiment, luxS mutant LW12 vs. wild type W3110
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Project description:Transcripitonal profiling of Escherichia coli K-12 W3110 comparing cells with and without hydrogen peroxide treatment, two biological replicates each One-condition experiment, cells with or without hydrogen peroxide treatment for 10min
2014-01-01 | E-GEOD-38185 | biostudies-arrayexpress
Project description:Here we present the study on ChIP-chip mapping of the genomic binding sites for Sty1, Atf1, and the Atf1's binding partner Pcr1; the genome-wide transcriptional profiling of the atf1 and pcr1 strains in response to H2O2; and the phenotypic assessment of ~90 Atf1/Pcr1-bound or unbound genes for growth fitness under H2O2 conditions. ChIP-chip analysis shows that Atf1 and Pcr1 binding sites are overlapped in the genome and constitutively present before H2O2 stress. On the other hand, Sty1 recruitment primarily occurs at the Atf1/Pcr1 binding sites and is induced by H2O2. We found that Atf1/Pcr1 is clearly responsible for the high-level transcriptional response to H2O2. Furthermore, phenotypic assessment indicates that among the H2O2-induced genes, Atf1/Pcr1-bound genes exhibit a higher likelihood of functional requirement for growth fitness under the stress condition than the Atf1/Pcr1-unbound genes do. Notably, we found that the Atf1/Pcr1-bound genes regardless of their responsiveness to H2O2 show a high probability of requirement for growth fitness. . Expression level of genes in triplicates at 0min (without stress) is compared with that at 10, 30, 60, and 120min after stress treatment. ChIP-chip analyses is done for Atf1-HA, pcr1-HA, sty1-HA, Sty1-HA allele in the atf1D or pcr1D background without and with H2O2 (0.5mM for 30min).
2010-07-19 | E-GEOD-13053 | biostudies-arrayexpress
Project description:Using data from microarray experiments, we investigated the effects of excess hydrogen peroxide on D. vulgaris. Keywords: stress response, time course Comparison of cells treated with 1 mM H2O2,sterile water Peroxide to untreated cells at times of 0,120,240,30,480,60 min.
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Project description:50mM H2O2 was added to mid-log phase Halobacterium NRC-1 cultures. After constant stress of H2O2 for 30 minutes, cultures were spun down and pellets were resuspended in same volume of GN101 media. Samples for RNA preparation were collected during recovery time points at 0, 10, 20, 30, 40, 60 and 120 minutes. 16 samples (8 exposed to H2O2 and 8 non-exposed controls) were each hybridized on duplicate arrays (as dye-flips) against the same standard control sample.
2010-05-27 | E-GEOD-7610 | biostudies-arrayexpress
Project description:GAPDHs from human pathogens S. aureus and P. aeruginosa can be readily inhibited by ROS-mediated direct oxidation of their catalytic active cysteines. Because of the rapid degradation of H2O2 by bacterial catalase, only steady-state but not one-dose treatment of H2O2 induces rapid metabolic reroute from glycolysis to pentose phosphate pathway (PPP). We conducted RNA-seq analyses to globally profile the bacterial transcriptomes in response to a steady level of H2O2, which reveals profound transcriptional changes including the induced expression of glycolytic genes in both bacteria. Our results revealed that the inactivation of GAPDH by H2O2 induces a metabolic reroute from glycolysis to PPP; the elevated levels of fructose 1,6-biphosphate (FBP) and 2-keto-3-deoxy-6-phosphogluconate (KDPG) lead to dissociation of their corresponding glycolytic repressors (GapR and HexR, respectively) from their cognate promoters, thus resulting in derepression of the glycolytic genes to overcome H2O2-stalled glycolysis in S. aureus and P. aeruginosa, respectively. Given that H2O2 can be produced constitutively by the host immune response, exposure to the steady-state stress of H2O2 recapitulates more accurately bacterial responses to host immune system in vivo. RNA-seq in Pseudomonas aeruginosa and Staphylococus aureus under steady state of H2O2
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2012-07-31 | E-GEOD-31053 | biostudies-arrayexpress
Project description:Transcripitonal profiling of Escherichia coli K-12 BW25113 comparing cells with isooctane treatment at time point of 0, 10, 30 and 60 min with two biological replicates One-condition experiment, cells with isooctane treatment at incubation time of 0, 10, 30 and 60 min, respectively
2014-09-13 | E-GEOD-32131 | biostudies-arrayexpress
Project description:Yersinia pestis (Y. pestis) is the etiologic agent of the plague, an endemic zoonotic disease of critical clinical and historic importance. The species belongs to a genus comprising eleven members, three of which are human pathogens. Y. pestis and its closest extant relative, Yersinia pseudotuberculosis, are very similar in many respects, yet there is a distinct dichotomy between these species in terms of pathogenicity. Y. pseudotuberculosis produces a relatively benign food- or water-borne gastroenteritis with rare cases of potentially fatal bacteremia. In contrast, the characteristics of high infectivity and high mortality have made Y. pestis a pathogen of historic importance with devastating effects on the human populace over the course of three major pandemics. These qualities coupled with the emergence of multi-drug resistant variants make Y. pestis an ideal candidate for use as a bioterrorism agent. Consequentially, evolutionary biology of this organism has become a priority in the counter-terrorism research effort. The flow of genetic information within the Y. pseudotuberculosis/Y. pestis group motivated us to identify novel genes for the purpose of creating a pan-genome species DNA microarray to better understand the phylogenomic relationships among its members. Based on the sequence information be generated from the novel gene discovery project conducted at the PFGRC as well as other publicly available sources regarding Yersinia spp. genome sequences, we designed a species microarray which represents the hitherto known genetic repertoire of this taxonomic group. In order to create a species microarray that represents novel genes or genes with significant sequence variation, the ArrayOligoSelector software (http://arrayoligosel.sourceforge.net/) was used to design a 70-mer oligonucleotide for each of the annotated ORFs or partial ORFs. A detailed description of the 70-mer oligo design process and filters developed by the PFGRC can be found on the PFGRC web site at (http://pfgrc.tigr.org/presentations/seminars/oligo_design_final.pdf). One hundred fifty six query strains were investigated in this study, with each query strain hybridized against the reference strain, CO92. Each strain has a single dye experiment. Each oligo is spotted on the Y. pestis species microarray once. Positive controls on the array consist of oligos designed from the sequenced reference genome, CO92, and negative controls on the array consist of oligos designed from the thale cress plant, Arabidopsis thaliana.The microarrays also had Agilent internal controls.
2010-09-02 | E-GEOD-23797 | biostudies-arrayexpress