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OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states

ABSTRACT: We performed evolution of Escherichia coli K12 MG1655 to study how the system adapt to iron toxicity. RNA-Seq was performed to examine the underlying transcriptional rewiring.

ORGANISM(S): Escherichia coli K-12

PROVIDER: GSE135516 | GEO | 2019/10/25

REPOSITORIES: GEO

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OxyR Is a Convergent Target for Mutations Acquired during Adaptation to Oxidative Stress-Prone Metabolic States.

Project description:Oxidative stress is concomitant with aerobic metabolism. Thus, bacterial genomes encode elaborate mechanisms to achieve redox homeostasis. Here we report that the peroxide-sensing transcription factor, oxyR, is a common mutational target using bacterial species belonging to two genera, Escherichia coli and Vibrio natriegens, in separate growth conditions implemented during laboratory evolution. The mutations clustered in the redox active site, dimer interface, and flexible redox loop of the protein. These mutations favor the oxidized conformation of OxyR that results in constitutive expression of the genes it regulates. Independent component analysis of the transcriptome revealed that the constitutive activity of OxyR reduces DNA damage from reactive oxygen species, as inferred from the activity of the SOS response regulator LexA. This adaptation to peroxide stress came at a cost of lower growth, as revealed by calculations of proteome allocation using genome-scale models of metabolism and macromolecular expression. Further, identification of similar sequence changes in natural isolates of E. coli indicates that adaptation to oxidative stress through genetic changes in oxyR can be a common occurrence.

| S-EPMC7038661 | biostudies-literature

Pseudogene repair driven by selection pressure applied in experimental evolution

Project description:We performed evolution of ∆menF∆entC strain of Escherichia coli K12 MG1655 to study how the system adapt to the loss of siderophore biosynthesis. RNA-Seq was performed to examine the underlying transcriptional rewiring.

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OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states

Project description:OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states

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Naphthoquinone-based aerobic respiration in E. coli

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Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity

Project description:We generated four strains of Escherichia coli K12 MG1655 with distinct proton motive force generation potential and performed the adaptive laboratory evolution of these strains to study how the system adapts to the loss of alternate electron transfer pathways of the Electron Transport System. RNA-Seq was performed to examine the underlying transcriptional rewiring.

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Deconvoluting Independent Regulatory Signals in the Escherichia coli Transcriptome

Project description:ChIPexo experiment was performed on E. coli K12 MG1655 with various supplements designed to activate transcriptional regulators

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Expression profiling to identify independent regulatory signals in Escherichia coli

Project description:RNA sequencing was performed on E. coli K12 MG1655 with various supplements designed to activate transcriptional regulators

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Expression profiling of E. coli in three media treated with antibiotics

Project description:RNA sequencing was performed on E. coli K12 MG1655 on three media (M9, CA-MHB, R10LB) treated with four antibiotics (Ciprofloxacin, Trimethoprim-sulfamethoxazole, Ceftriaxone, Meropenem) at their media-specific MIC90s

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ChIP-Seq experiment for the global regulators, CRP and Fis in early and mid exponential growth phases

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Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol

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