A model-driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K-12 MG1655 that is biochemically and thermodynamically consistent (Q44022674)

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English	A model-driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K-12 MG1655 that is biochemically and thermodynamically consistent	scientific article

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Europe PubMed Central

PubMed publication ID

29 November 2017

A model-driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K-12 MG1655 that is biochemically and thermodynamically consistent (English)

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Europe PubMed Central

PubMed publication ID

29 November 2017

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Escherichia coli str. K-12 substr. MG1655

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Bernhard Palsson

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Bernhard O Palsson

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Europe PubMed Central

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29 November 2017

Robert K Naviaux

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Robert K Naviaux

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29 November 2017

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Adam M Feist

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29 November 2017

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Zachary A King

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Europe PubMed Central

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29 November 2017

Douglas McCloskey

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Douglas McCloskey

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29 November 2017

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Jon A Gangoiti

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29 November 2017

Bruce A Barshop

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29 November 2017

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19 November 2013

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29 November 2017

Biotechnology and Bioengineering

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29 November 2017

111

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29 November 2017

4

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29 November 2017

803-815

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29 November 2017

An automated, pressure-driven sampling device for harvesting from liquid cultures for genomic and biochemical analyses.

1 reference

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Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach

1 reference

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An overlap between osmotic and anaerobic stress responses: a potential role for DNA supercoiling in the coordinate regulation of gene expression

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A RAPID METHOD OF TOTAL LIPID EXTRACTION AND PURIFICATION

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Sampling for metabolome analysis of microorganisms.

1 reference

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FNR-mediated oxygen-responsive regulation of the nrdDG operon of Escherichia coli

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21 January 2018

Ultrahigh performance liquid chromatography-tandem mass spectrometry method for fast and robust quantification of anionic and aromatic metabolites

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21 January 2018

Synergy between (13)C-metabolic flux analysis and flux balance analysis for understanding metabolic adaptation to anaerobiosis in E. coli.

1 reference

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Altered topoisomerase activities may be involved in the regulation of DNA supercoiling in aerobic-anaerobic transitions in Escherichia coli.

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Engineered reversal of the β-oxidation cycle for the synthesis of fuels and chemicals

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In silico design and adaptive evolution of Escherichia coli for production of lactic acid.

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Quinones as the redox signal for the arc two-component system of bacteria

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Glucose-6-phosphate dehydrogenase and ferredoxin-NADP(H) reductase contribute to damage repair during the soxRS response of Escherichia coli.

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A novel regulatory mechanism couples deoxyribonucleotide synthesis and DNA replication in Escherichia coli.

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Bacterial redox sensors.

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Thermodynamics-based metabolic flux analysis

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Ribonucleotide reductase and the regulation of DNA replication: an old story and an ancient heritage.

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Fast sampling and quenching procedures for microbial metabolic profiling

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Cellular defenses against superoxide and hydrogen peroxide

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Multiple high-throughput analyses monitor the response of E. coli to perturbations

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Genetic and molecular characterization of the genes involved in short-chain fatty acid degradation in Escherichia coli: the ato system

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Metabolite essentiality elucidates robustness of Escherichia coli metabolism

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Metabolic fluxes during strong carbon catabolite repression by malate in Bacillus subtilis

1 reference

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21 January 2018

The soxRS response of Escherichia coli can be induced in the absence of oxidative stress and oxygen by modulation of NADPH content

1 reference

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21 January 2018

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

1 reference

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Adenylate kinase complements nucleoside diphosphate kinase deficiency in nucleotide metabolism

1 reference

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21 January 2018

The gene for nucleoside diphosphate kinase functions as a mutator gene in Escherichia coli.

1 reference

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21 January 2018

Metabolomic analysis via reversed-phase ion-pairing liquid chromatography coupled to a stand alone orbitrap mass spectrometer

1 reference

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The alternative aerobic ribonucleotide reductase of Escherichia coli, NrdEF, is a manganese‐dependent enzyme that enables cell replication during periods of iron starvation

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21 January 2018

Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli

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Network context and selection in the evolution to enzyme specificity.

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A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011.

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Regulation of the citrate synthase (gltA) gene of Escherichia coli in response to anaerobiosis and carbon supply: role of the arcA gene product

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21 January 2018

Escherichia coli transcriptome dynamics during the transition from anaerobic to aerobic conditions

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21 January 2018

Cloning of the two pyruvate kinase isoenzyme structural genes from Escherichia coli: the relative roles of these enzymes in pyruvate biosynthesis

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Acidic acetonitrile for cellular metabolome extraction from Escherichia coli.

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Inhibition of Escherichia coli growth by acetic acid: a problem with methionine biosynthesis and homocysteine toxicity.

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Transcript profiling and inference of Escherichia coli K-12 ArcA activity across the range of physiologically relevant oxygen concentrations

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Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA.

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The soluble and membrane-bound transhydrogenases UdhA and PntAB have divergent functions in NADPH metabolism of Escherichia coli

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21 January 2018

Integrated sampling procedure for metabolome analysis

1 reference

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Effect of ArcA and FNR on the expression of genes related to the oxygen regulation and the glycolysis pathway in Escherichia coli under microaerobic growth conditions

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21 January 2018

Effect of oxygen, and ArcA and FNR regulators on the expression of genes related to the electron transfer chain and the TCA cycle in Escherichia coli

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Development and application of a differential method for reliable metabolome analysis in Escherichia coli.

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Escherichia coli responds with a rapid and large change in growth rate upon a shift from glucose-limited to glucose-excess conditions

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Regulation of aerobic-to-anaerobic transitions by the FNR cycle in Escherichia coli

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Metabolic regulation analysis of wild-type and arcA mutant Escherichia coli under nitrate conditions using different levels of omics data.

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Reprogramming of Escherichia coli K-12 metabolism during the initial phase of transition from an anaerobic to a micro-aerobic environment

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Homocysteine toxicity in Escherichia coli is caused by a perturbation of branched-chain amino acid biosynthesis

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Flux through citrate synthase limits the growth of ethanologenic Escherichia coli KO11 during xylose fermentation

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Lack of protective osmolytes limits final cell density and volumetric productivity of ethanologenic Escherichia coli KO11 during xylose fermentation

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Condition-dependent cell volume and concentration of Escherichia coli to facilitate data conversion for systems biology modeling

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An anchoring role for FeS clusters: chelation of the amino acid moiety of S-adenosylmethionine to the unique iron site of the [4Fe-4S] cluster of pyruvate formate-lyase activating enzyme

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Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites.

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Quantitative analysis of the microbial metabolome by isotope dilution mass spectrometry using uniformly 13C-labeled cell extracts as internal standards

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anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data

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Cross-platform comparison of methods for quantitative metabolomics of primary metabolism

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Identifiers

10.1002/BIT.25133

1 reference

Europe PubMed Central

PubMed publication ID

29 November 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

29 November 2017

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