Experimental evolution reveals the genetic basis and systems biology of superoxide stress tolerance
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ABSTRACT:
ORGANISM(S): Escherichia coli
PROVIDER: GSE134256 | GEO | 2022/07/07
REPOSITORIES: GEO
Similar Datasets
Project description:We use adaptive laboratory evolution to generate strains which tolerate high levels of the redox cycling compound paraquat, which produces reactive oxygen species (ROS). We combine resequencing, iModulon analysis of the transcripome, and metabolic models to elucidate six interacting stress tolerance mechanisms: 1) modification of transport, 2) activation of ROS stress responses, 3) use of ROS-sensitive iron regulation, 4) motility, 5) broad transcriptional reallocation toward growth, and 6) metabolic rewiring to decrease NADH production. This work thus reveals the genome-scale systems biology of ROS tolerance.
2022-12-19 | GSE221314 | GEO
Project description:Escherichia coli O157 presents a number of specific problems in terms of food safety and public health. It has been found that E. coli O157 is more resistant to a number of the stresses encountered during food production such as heat, pH and osmotic shock. This greater resistance is thought to contribute to the low infectious dose of E. coli O157 (<100 organisms). Moreover, E. coli O157 is associated with debilitating conditions such as haemorrhagic colitis and haemoytic uraemic syndrome, particularly in children and the elderly. We have been studying the stress responses of E. coli O157:H7 (Sakai) and comparing with a commensal strain of E. coli K-12, MG1655. We found that E. coli O157 (Sakai) is more sensitive to oxidative stress than MG1655. A microarray study of these strains treated with sub-lethal concentrations (0.5mg/ml) of menadione revealed big differences in their responses. In E. coli O157 (Sakai), 540 genes responded significantly to the treatment compared to 121 genes in MG1655. One surprising finding from the microarray data was the observation that many iron-transport genes were up-regulated in E. coli O157 (Sakai) whereas relatively few were induced in MG1655 despite the fact that the bacteria were grown in a medium containing ample iron. We speculated that the induction of iron transport genes in an iron-rich medium might have contributed to the enhanced killing of E. coli O157 (Sakai) through triggering of a Fenton reaction. We speculated that the difference in sensitivity to oxidative stress might be due to differences in the intracellular iron content of E. coli O157 and MG1655. We found that E. coli O157 contains ~50% more iron than MG1655 and believe that during oxidative stress, this iron is released by damaged proteins. The greater levels of free iron in E. coli O157 will trigger a greater Fenton reaction that can damage the ferric uptake regulator (Fur), resulting in unregulated iron transport. In MG1655, the lower iron content results in a smaller Fenton reaction, enabling the cellular protection systems to limit damage and protect Fur.
2015-02-22 | GSE36130 | GEO
Project description:Superoxide radical anion and other Reactive Oxygen Species are constantly produced during respiration. In mitochondria, the dismutation of the superoxide radical anion is accelerated by the mitochondrial superoxide dismutase 2 (SOD2), an enzyme that has been traditionally associated with antioxidant protection. However, increases in SOD2 expression promote oxidative stress, indicating that there may be a prooxidant role for SOD2. We show that SOD2, which normally binds manganese, can incorporate iron and generate an alternative isoform with peroxidase activity. The switch from manganese to iron allows FeSOD2 to utilize H2O2 to promote oxidative stress. We found that FeSOD2 is formed in cultured cells. FeSOD2 causes mitochondrial dysfunction and higher levels of oxidative stress in cultured cells. We show that formation of FeSOD2 converts an antioxidant defense into a prooxidant peroxidase that leads to cellular changes seen in multiple human diseases.
2017-12-05 | GSE106206 | GEO
Project description:Escherichia coli O157 presents a number of specific problems in terms of food safety and public health. It has been found that E. coli O157 is more resistant to a number of the stresses encountered during food production such as heat, pH and osmotic shock. This greater resistance is thought to contribute to the low infectious dose of E. coli O157 (<100 organisms). Moreover, E. coli O157 is associated with debilitating conditions such as haemorrhagic colitis and haemoytic uraemic syndrome, particularly in children and the elderly. We have been studying the stress responses of E. coli O157:H7 (Sakai) and comparing with a commensal strain of E. coli K-12, MG1655. We found that E. coli O157 (Sakai) is more sensitive to oxidative stress than MG1655. A microarray study of these strains treated with sub-lethal concentrations (0.5mg/ml) of menadione revealed big differences in their responses. In E. coli O157 (Sakai), 540 genes responded significantly to the treatment compared to 121 genes in MG1655. One surprising finding from the microarray data was the observation that many iron-transport genes were up-regulated in E. coli O157 (Sakai) whereas relatively few were induced in MG1655 despite the fact that the bacteria were grown in a medium containing ample iron. We speculated that the induction of iron transport genes in an iron-rich medium might have contributed to the enhanced killing of E. coli O157 (Sakai) through triggering of a Fenton reaction. We speculated that the difference in sensitivity to oxidative stress might be due to differences in the intracellular iron content of E. coli O157 and MG1655. We found that E. coli O157 contains ~50% more iron than MG1655 and believe that during oxidative stress, this iron is released by damaged proteins. The greater levels of free iron in E. coli O157 will trigger a greater Fenton reaction that can damage the ferric uptake regulator (Fur), resulting in unregulated iron transport. In MG1655, the lower iron content results in a smaller Fenton reaction, enabling the cellular protection systems to limit damage and protect Fur. Overnight cultures of E. coli O157 (Sakai) and E. coli K-12 MG1655 were grown in Neidhardt's EZ Rich Defined Medium and diluted 1:100 in 50 ml fresh medium in 125 ml Ehrlenmeyer flasks. The cultures were shaken at 37C until the optical density (OD600) reached 0.4. Each culture was divided into 2 equal parts in identical flasks. One flask contained menadione bisulphite to a final concentration of 0.5 mg/ml; the other flask contained an equivalent volume of distilled water. The flasks were shaken for a further 10 mins and then treated with RNAprotect™ to stabilise the mRNA. The experiment was performed 3 times on different days. Six custom-made microarray slides were used in this study; each slide was hybridised with labelled cDNA made from mRNA taken from untreated and treated E. coli O157 (Sakai) or MG1655.
2015-02-22 | E-GEOD-36130 | biostudies-arrayexpress
Project description:Benzalkonium chloride (BC) is a commonly used disinfectant and preservative. This study describes changes in expression level on the transcriptomic and proteomic level for Escherichia coli K12 gradually adapted to a tolerance level towards BC of 7-8 times the initial MIC. Results from DNA arrays and two-dimensional (2-DE) gel electrophoresis for global gene and protein expression studies were confirmed by real time quantitative PCR. Peptide mass fingerprinting by MALDI-TOF MS was used to identify differentially expressed proteins. Changes in expression level in adapted cells were shown for porins, drug transporters, glycolytic enzymes, ribosomal subunits and several genes and proteins involved in protection against oxidative stress and antibiotics. Adapted strains showed increased tolerance to several antibiotics. In conclusion, E. coli K12 adapted to higher tolerance to BC, acquired several general resistance mechanisms including responses normally related to the multiple antibiotic resistance (Mar) regulon and protection against oxidative stress. The results revealed that BC treatment might result in superoxide stress in E. coli. Keywords: Study of resistance mechanism
2007-05-23 | GSE6712 | GEO
Project description:Profiled the effect of oxidative stress on gene expression in the heads of adult Drosophila. The flies were fed sucrose with 15mM paraquat (experimental condition) or regular sucrose (control condition) for 30 hours, before harvesting at adult d3. Keywords = oxidative stress Keywords = paraquat Keywords: dose response
2004-01-18 | GSE827 | GEO
Project description:Background: Pseudomonas aeruginosa, a pathogen infecting those with cystic fibrosis, encounters toxicity from phagocyte-derived reactive oxidants including hydrogen peroxide during active infection. P. aeruginosa responds with adaptive and protective strategies against these toxic species to effectively infect humans. Despite advances in our understanding of the responses to oxidative stress in many specific cases, the connectivity between targeted protective genes and the rest of cell metabolism remains obscure. Results: Herein, we performed a genome-wide transcriptome analysis of the cellular responses to hydrogen peroxide in order to determine a more complete picture of how oxidative stress-induced genes are related and regulated. Our data reinforce the previous conclusion that DNA repair proteins and catalases may be among the most vital antioxidant defense systems of P. aeruginosa. Our results also suggest that sublethal oxidative damage reduces active and/or facilitated transport and that intracellular iron might be a key factor for a relationship between oxidative stress and iron regulation. Perhaps most intriguingly, we revealed that the transcription of all F-, R-, and S-type pyocins was upregulated by oxidative stress and at the same time, a cell immunity protein (pyocin S2 immunity protein) was downregulated, possibly leading to self-killing activity. Conclusions: This finding proposes that pyocin production might be another novel defensive scheme against oxidative attack by host cells. Experiment Overall Design: We conducted four and five independent microarray experiments with biological replicates in the absence (control) and the presence (experimental) of hydrogen peroxide, respectively.
2007-07-19 | E-GEOD-3090 | biostudies-arrayexpress
Project description:To understand the mechanism of isopropanol tolerance of Escherichia coli for improvement of isopropanol production, we performed genome re-sequencing and transcriptome analysis of isopropanol tolerant E. coli strains obtained from parallel adaptive laboratory evolution under IPA stress.
2017-06-21 | GSE89685 | GEO
Project description:SIN3 the scaffold protein of a histone deacetylase complex interacts with a histone demethylase KDM5 (little imaginal discs - LID) in Drosophila. Reduction of SIN3 or dKDM5/LID both result in similar phenotypes during cell proliferation and wing development. To identify underlying transcriptional changes that may contribute to these phentypic defects we performed whole genome expression analysis in Drosophila cultured cells upon RNAi-mediated knockdown of Sin3A, lid or both. We identified a large number of genes regulated by SIN3, dKDM5/LID or both. While many common genes were regulated by SIN3 and dKDM5/LID an enrichment for genes involved in stress tolerance pathways was observed. Additional RNAseq analysis of expression changes upon knockdown of Sin3A, lid or both under paraquat mediated oxidative stress conditions identified significant changes in genes involved in cell cycle related processes. Drosophila S2 cells were treated with dsRNA targetting Sin3A, lid and both or GFP as control under normal or oxidative stress conitions induced by treatment with paraquat. mRNA profiling of these samples were performed by deep sequencing using Illumina Hiseq2500.Three biological replicates were performed.
2016-01-09 | E-GEOD-68775 | biostudies-arrayexpress
Project description:A deeper understanding of malaria parasite development inside the Anopheles mosquito may lead to the identification of processes that can be targeted by transmission-blocking interventions. Paraquat (1,1'-dimethyl-4,4'-bipyridylium dichloride) is a potent superoxide-inducing agent that impacts Plasmodium ookinete development, especially at higher concentrations. Compounds like Paraquat can potentially induce an oxidative imbalance in the mosquito midgut during ookinete maturation, essentially super-stressing the parasite leading to the arrested development of ookinetes, the only stage that can invade through a mosquito midgut cell to establish an oocyst infection in the mosquito. The mosquito midgut has evolved to handle the natural production of reactive oxygen and nitrogen species (ROS and RNS, respectively) as a result of feeding on blood. The addition of Paraquat to a bloodmeal is expected to induce a cognate response in the midgut to handle the excess ROS/RNS, and high concentrations of this compound can potentially overwhelm the midgut response leading to mosquito death. While several studies have explored the effect of Paraquat on malaria parasites, a fundamental understanding of the mosquito response to this compound remains unknown. Here, we quantified the mosquito midgut proteomic response to a Paraquat-laced sugar meal to understand the intrinsic midgut response (in the absence of a bloodmeal). We then carried out transcriptomic analysis of the mosquito midgut for several antioxidants of the Trx and GSH pathways to compare concordance or discordance between protein and its transcripts during different oxidative stress conditions. Finally, we determined whether the same Trx and GSH pathways are upregulated following infection with either P. falciparum or P. berghei at 24 hrs post-blood feeding, coinciding with the time point for maximal ookinete traversal of the midgut. We discuss the potential selective action of Paraquat on the parasite and the intrinsic tolerance of the mosquito midgut to Paraquat-mediated oxidative stress.
2022-03-01 | PXD008231 | Pride