Escherichia coli
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA94823 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Balanced growth of Ecoli MG1655/pTrc99a(NOX-) at different growth rates
| PRJNA94825 | ENA
Project description:Responses of Escherichia coli MG1655/pTrc99a(NOX+) grown at different growth rates in chemostat in M9 + salts NOX: NADH oxygenase converts NADH to NAD. Cells with NOX are able to recycle the excess NADH generated during rapid growth, leading to lesser accumulation of acetate Keywords: different growth rates in parallel
2006-03-08 | GSE4365 | GEO
Project description:Responses of Escherichia coli MG1655/pTrc99a(NOX-) grown at different growth rates in chemostat in M9 + salts Keywords: different growth rates in parallel
2006-03-08 | GSE4366 | GEO
Project description:Metabolic cofactors such as NADH and ATP play important roles in a large number of cellular reactions and it is of great interest to dissect the role of these cofactors in different aspects of metabolism. Towards this goal, we overexpressed NADH oxidase and the soluble F1-ATPase in Escherichia coli to lower the level of NADH and ATP, respectively. We used a systems biology approach to study the response to these perturbations by measuring global transcription profiles, metabolic fluxes and the metabolite levels. We integrated information from the different measurements using network-based methods to identify high-scoring networks in a global interaction map that included protein interactions, transcriptional regulation and metabolism. The results revealed that the action of many global transcription factors such as ArcA, Fnr, CRP and IHF commonly involved both NADH and ATP while others were influential only in one of the pertubations. In general, overexpressing NADH oxidase invokes response in widespread aspects of metabolism involving the redox cofactors (NADH and NADPH) while ATPase has a more focused response to restore ATP level by enhancing proton translocation mechanisms and repressing biosynthesis. Interestingly, NADPH played a key role in restoring redox homeostasis through the concerted activity of isocitrate dehydrogenase and UdhA transhydrogenase. We present a reconciled network of regulation that illustrates the overlapping and distinct aspects of metabolism controlled by NADH and ATP. Our study contributes to the general understanding of redox and energy metabolism and should help in developing metabolic engineering strategies in E. coli. The experimental design involves measuring transcriptome in three strains (in triplicates) of E. coli during mid-exponential phase of growth on MOPS media supplemented with glucose. The three strains are: 1. REF: MG1655/pAK80 (MG1655 transformed with a plasmid with no insert) 2. NOX: MG1655/pAC06 (MG1655 transformed with a plasmid containing NADH oxidase) 3. ATPase: MG1655/pCP41 (MG1655 transformed with a plasmid containing soluble ATPase) RNA was extracted using Qiagen RNeasy kit and processes according to Affymetrix® guidelines. The quality of RNA was verified using BioAnalyzer (Agilent BioSystems) and the electropherograms are shown in the file âRNA quality.pdfâ. Samples 1-3 are REF, Samples 4-6 are NOX and Samples 7-9 are ATPase. The fragmented cRNA was hybridized to E. coli Genome 2.0 chips.
2010-02-21 | E-GEOD-20374 | biostudies-arrayexpress
Project description:Gene expression profile of E. coli MG1655 cells grown at different growth rates in mixed substrates culture
| PRJNA223609 | ENA
Project description:Transcription profiling of E. coli MG1655, representing the effect of G181D/R258C NusA in comparison to WT NusA Agilent one-color experiment,Organism: Escherichia coli ,Agilent Custom Ecoli Gene Expression Microarray 2x400k designed by Genotypic Technology Private Limited. (AMADID:72220)
2016-03-28 | E-GEOD-77009 | biostudies-arrayexpress
Project description:Supernatant from B. subtilis cultures was found to be inhibitory to E. coli MG1655 growth and reduce enrichment of nitrofurantoin-resistant strains in the presence of the antibiotic. Supernatant from six different supernatants with differential effects on E. coli growth was harvested and analysed to identify the protein component responsible for growth inhibition.
2023-03-15 | PXD040869 | Pride
Project description:Mapping the occupancy of ArcA throughout the genome of Escherchia coli MG1655 K-12 using an affinity purified antibody under anaerobic and aerobic growth conditions. As a control, we also performed ChIP-chip onArcA in a ∆arcA mutant strain of Escherchia coli MG1655 K-12. Described in the manuscript The response regulator ArcA uses a diverse binding site architechture to globally regulate carbon oxidation in E. coli
2013-10-17 | GSE46413 | GEO
Project description:Mapping the occupancy of FNR, HNS, and IHF throughout the genome of Escherchia coli MG1655 K-12 using an affinity purified antibody under anerobic growth conditions. We also mapped the binding of the ß subunit of RNA Polymerase under both aerobic and anaerobic growth conditions. As a control, we also performed ChIP-chip on FNR in a ∆fnr mutant strain of Escherchia coli MG1655 K-12. We also examined FNR immunoprecipitation at various FNR concentrations using IPTG and Ptac::fnr (PK8263). The ∆hns/∆stpA strains were also used. Descirbed in the manuscript Genome-scale Analysis of E. coli FNR Reveals the Complexity of Bacterial Regulon Structure
2013-06-20 | GSE41186 | GEO
Project description:ChIPexo experiment was performed on E. coli K12 MG1655 with various supplements designed to activate transcriptional regulators
2019-12-17 | GSE122320 | GEO