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Transcriptome analysis of wild type E. coli (K-12 MG1655) comparing to mutant E. coli strain (ECOM4) under aerobic and anaerobic conditions

ABSTRACT: Cytochrome oxydases and quinol monooxygenase were removed from the E. coli genome resulting in oxygen-independent physiology We used microarray profiling to identify perturbed metabolic or regulatory functionality resulting in the inability to undergo aerobic-anaerobic shift.

ORGANISM(S): Escherichia coli Escherichia coli str. K-12 substr. MG1655

PROVIDER: GSE21839 | GEO | 2010/10/15

SECONDARY ACCESSION(S): PRJNA126925

REPOSITORIES: GEO

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Transcriptome analysis of wild type E. coli (K-12 MG1655) comparing to mutant E. coli strain (ECOM4) under aerobic and anaerobic conditions

Project description:Cytochrome oxydases and quinol monooxygenase were removed from the E. coli genome resulting in oxygen-independent physiology We used microarray profiling to identify perturbed metabolic or regulatory functionality resulting in the inability to undergo aerobic-anaerobic shift. Affimetrics E. coli Arrays 2.0, Experiment (ECOM4) under both conditions (+O2/-O2) were analyzed in triplicates and compared to control (MG1655) under same conditions in triplicates

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Expression analysis of Escherichia coli MG1655 K-12 ∆hns/∆stpA from aerobic and anaerobic growth conditions

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Genome-wide analysis of FNR and σ70 in E. coli under aerobic and anaerobic growth conditions.

Project description:We found many binding sites for FNR under glucose fermentative anaerobic growth conditions. Also, many binding sites were identified for σ70 under both aerobic and anaerobic growthin conditions. Descirbed in the manuscript "Genome-scale Analysis of E. coli FNR Reveals the Complexity of Bacterial Regulon Structure"

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Expression analysis of Escherichia coli MG1655 K-12 M-bM-^HM-^Fhns/M-bM-^HM-^FstpA from aerobic and anaerobic growth conditions

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Deletion of genes encoding cytochrome oxidases and quinol monooxygenase blocks the aerobic-anaerobic shift in Escherichia coli K-12 MG1655.

Project description:The constitutive activation of the anoxic redox control transcriptional regulator (ArcA) in Escherichia coli during aerobic growth, with the consequent production of a strain that exhibits anaerobic physiology even in the presence of air, is reported in this work. Removal of three terminal cytochrome oxidase genes (cydAB, cyoABCD, and cbdAB) and a quinol monooxygenase gene (ygiN) from the E. coli K-12 MG1655 genome resulted in the activation of ArcA aerobically. These mutations resulted in reduction of the oxygen uptake rate by nearly 98% and production of d-lactate as a sole by-product under oxic and anoxic conditions. The knockout strain exhibited nearly identical physiological behaviors under both conditions, suggesting that the mutations resulted in significant metabolic and regulatory perturbations. In order to fully understand the physiology of this mutant and to identify underlying metabolic and regulatory reasons that prevent the transition from an aerobic to an anaerobic phenotype, we utilized whole-genome transcriptome analysis, (13)C tracing experiments, and physiological characterization. Our analysis showed that the deletions resulted in the activation of anaerobic respiration under oxic conditions and a consequential shift in the content of the quinone pool from ubiquinones to menaquinones. An increase in menaquinone concentration resulted in the activation of ArcA. The activation of the ArcB/ArcA regulatory system led to a major shift in the metabolic flux distribution through the central metabolism of the mutant strain. Flux analysis indicated that the mutant strain had undetectable fluxes around the tricarboxylic acid (TCA) cycle and elevated flux through glycolysis and anaplerotic input to oxaloacetate. Flux and transcriptomics data were highly correlated and showed similar patterns.

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Project description:The changes in protein composition of E. coli were studied in a global proteomic approach for aerobic growth without or with fumarate as carbon source (glycerol + O2, fumarate + O2, respectively) and anaerobic growth without or with fumarate as carbon source (glycerol + DMSO, glycerol + DMSO + fumarate, respectively). The experiments should unravel the changes in response to fumarate under aerobic (i) and anaerobic (ii) conditions, and more generally (iii) the fumarate proteome under aerobic versus anaerobic conditions. Fumarate was used as the C4DC due to its capability to support aerobic and anaerobic growth, and glycerol was used as the alternative carbon source that exerts no or only weak carbon catabolite repression.

2019-11-20 | PXD011760 | Pride

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