Response of the central metabolism of <i>Escherichia coli</i> to modified expression of the gene encoding the glucose‐6‐phosphate dehydrogenase

Nicolas, Cécile; Kiefer, Patrick; Létisse, Fabien; Krömer, Jens O.; Massou, Stéphane; Soucaille, Philippe; Wittmann, Christoph; Lindley, Nic D.; Portais, Jean‐Charles

doi:10.1016/j.febslet.2007.06.066

Cited by 63 publications

(74 citation statements)

References 25 publications

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“…The genetic perturbation experiments showed that out of 60 metabolic genes, only 3 were lethal and 5 affected strongly the growth rate on glucose. Consistent with previous work (29,37,42), these results highlight the robustness of E. coli metabolism despite loss of a single enzyme in central carbon metabolism. Thanks to physiological descriptors, we were able to reveal not only the phenotype of silent mutations, in terms of growth, but also the phenotype of gene deletion mutants not directly involved in central metabolism (i.e., transcription and sigma factors).…”

Section: Discussionsupporting

confidence: 80%

High-Throughput Workflow for Monitoring and Mining Bioprocess Data and Its Application to Inferring the Physiological Response of Escherichia coli to Perturbations

Heux

Philippe

Portais

2011

Appl Environ Microbiol

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Miniaturization and high-throughput screening are currently the focus of emerging research areas such as systems biology and systems biotechnology. A fluorescence-based screening assay for the online monitoring of oxygen and pH and a numerical method to mine the resulting online process data are described. The assay employs commercial phosphorescent oxygen-and pH-sensitive probes in standard 48-or 96-well plates on a plate reader equipped with a shaker. In addition to dual parametric analysis of both pH and oxygen in a single well, the assay allows monitoring of growth, as measured by absorbance. Validation of the assay is presented and compared with commercially available plates equipped with optical sensors for oxygen and pH. By using model-free fitting to the readily available online measurements, the length and rate of each phase such as the duration of lag and transition phase or acidification, growth, and oxygen consumption rates are automatically detected. In total, nine physiological descriptors, which can be used for further statistical and comparison analysis, are extracted from the pH, oxygen partial pressure (pO 2 ), and optical density (OD) profiles. The combination of a simple mix-and-measure procedure with an automatic data mining method allows high sample throughput and good reproducibility while providing a physiological state identification and characterization of test cells. As a proof of concept, the utility of the workflow in assessing the physiological response of Escherichia coli to environmental and genetic perturbations is demonstrated.

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Section: Discussionsupporting

confidence: 80%

High-Throughput Workflow for Monitoring and Mining Bioprocess Data and Its Application to Inferring the Physiological Response of Escherichia coli to Perturbations

Heux

Philippe

Portais

2011

Appl Environ Microbiol

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“…F6P is a precursor for a range of biomolecules, including peptidoglycan and lipid A, and cannot be used as a substrate for glycolysis because the Caulobacter genome does not encode a phosphofructokinase (9). It has been shown experimentally that decreased zwf expression in Escherichia coli modulates carbon flux through central metabolic pathways, resulting in increased concentrations of F6P (29). Similarly, synthesis of the exopolysaccharide alginate in Pseudomonas aeruginosa requires F6P as a precursor (38).…”

Section: Vol 192 2010 Genetic Basis Of Caulobacter Adaptation 3683mentioning

confidence: 99%

The Genetic Basis of Laboratory Adaptation in Caulobacter crescentus

et al. 2010

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The dimorphic bacterium Caulobacter crescentus has evolved marked phenotypic changes during its 50-year history of culture in the laboratory environment, providing an excellent system for the study of natural selection and phenotypic microevolution in prokaryotes. Combining whole-genome sequencing with classical molecular genetic tools, we have comprehensively mapped a set of polymorphisms underlying multiple derived phenotypes, several of which arose independently in separate strain lineages. The genetic basis of phenotypic differences in growth rate, mucoidy, adhesion, sedimentation, phage susceptibility, and stationary-phase survival between C. crescentus strain CB15 and its derivative NA1000 is determined by coding, regulatory, and insertion/deletion polymorphisms at five chromosomal loci. This study evidences multiple genetic mechanisms of bacterial evolution as driven by selection for growth and survival in a new selective environment and identifies a common polymorphic locus, zwf, between lab-adapted C. crescentus and clinical isolates of Pseudomonas aeruginosa that have adapted to a human host during chronic infection.Colonization of new environments or changes in resource availability, predatory regime, or climate can drive adaptive evolution. Determining the genetic basis of these changes informs our understanding of the evolution of diversity and the nature of selection. Domestication of crop plants, adaptive radiations, and in-host evolution during chronic microbial infection are characterized by the evolution of a suite of phenotypes that are advantageous in the new environment. Recent work has successfully identified several of the polymorphisms responsible for this type of adaptive evolution in a variety of species (3,7,11,12,15,22,25,(35)(36)(37). With comparative genome sequencing emerging as a powerful tool for identifying genetic polymorphism (5, 14, 23), these studies are becoming faster and easier. Still, large genome sizes and countless sequence differences between individuals, isolates, strains, and species have made comprehensive analyses intractable.Upon isolation and introduction into the laboratory, model research organisms experience extreme environmental changes, with associated selection pressures. Indeed, adaptation to life in captivity has been observed in a wide range of domesticated and model research organisms (2) and in zoo populations of endangered species (31). Many phenotypes that evolve in these nonnative environments do so repeatedly and become common features of human-cultured, -raised, or -cultivated organisms (2), providing evidence of positive selection. Likewise, the aquatic bacterium Caulobacter crescentus has evolved marked phenotypic changes during the 50 years it has been cultured in the laboratory environment. At least six phenotypic differences (Fig. 1) between two closely related strains (NA1000 and CB15) derived from the same common ancestor have evolved over decades of laboratory cultivation. It is presumed that these phenotypes evolved in response to the dy...

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“…In the case of the partitioning of the flux around glucose-6-phosphate, it was observed that it does change after an increase in the demand (Rui et al, 2010) or the offer of NADPH (Martínez et al, 2008). To the best of our knowledge, there are no studies on how much control EcG6PDH could exert upon the flux through the oxPPP, although increasing its concentration above the typical level did not increase significantly the flux through this pathway (Nicolas et al, 2007;Orthner & Pizer, 1974). …”

Section: Design and Kinetic Study Of An Nad-preferring G6pdhmentioning

confidence: 99%

Metabolic impact of an NADH-producing glucose-6-phosphate dehydrogenase in Escherichia coli

et al. 2014

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In Escherichia coli, the oxidative branch of the pentose phosphate pathway (oxPPP) is one of the major sources of NADPH when glucose is the sole carbon nutrient. However, unbalanced NADPH production causes growth impairment as observed in a strain lacking phosphoglucoisomerase (Dpgi). In this work, we studied the metabolic response of this bacterium to the replacement of its glucose-6-phosphate dehydrogenase (G6PDH) by an NADH-producing variant. The homologous enzyme from Leuconostoc mesenteroides was studied by molecular dynamics and site-directed mutagenesis to obtain the NAD-preferring LmG6PDH R46E,Q47E . Through homologous recombination, the zwf loci (encoding G6PDH) in the chromosomes of WT and Dpgi E. coli strains were replaced by DNA encoding LmG6PDH R46E,Q47E . Contrary to some predictions performed with flux balance analysis, the replacements caused a substantial effect on the growth rates, increasing 59 % in the Dpgi strain, while falling 44 % in the WT. Quantitative PCR (qPCR) analysis of the zwf locus showed that the expression level of the mutant enzyme was similar to the native enzyme and the expression of genes encoding key enzymes of the central pathways also showed moderate changes among the studied strains. The phenotypic and qPCR data were integrated into in silico modelling, showing an operative G6PDH flux contributing to the NADH pool. Our results indicated that, in vivo, the generation of NADH by G6PDH is beneficial or disadvantageous for growth depending on the operation of the upper Embden-Meyerhof pathway. Interestingly, a genomic database search suggested that in bacteria lacking phosphofructokinase, the G6PDHs tend to have similar preferences for NAD and NADP. The importance of the generation of NADPH in a pathway such as the oxPPP is discussed.

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Response of the central metabolism of Escherichia coli to modified expression of the gene encoding the glucose‐6‐phosphate dehydrogenase

Cited by 63 publications

References 25 publications

High-Throughput Workflow for Monitoring and Mining Bioprocess Data and Its Application to Inferring the Physiological Response of Escherichia coli to Perturbations

High-Throughput Workflow for Monitoring and Mining Bioprocess Data and Its Application to Inferring the Physiological Response of Escherichia coli to Perturbations

The Genetic Basis of Laboratory Adaptation in Caulobacter crescentus

Metabolic impact of an NADH-producing glucose-6-phosphate dehydrogenase in Escherichia coli

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