Characterization of E. coli MG1655 and frdA and sdhC mutants at various aerobiosis levels

Steinsiek, Sonja; Frixel, Susanne; Stagge, Stefan; Bettenbrock, Katja

doi:10.1016/j.jbiotec.2011.03.015

Cited by 33 publications

(40 citation statements)

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“…3. This linear relationship between the specific ATP production rate and the specific growth rate held not only under aerobic conditions but also under micro-aerobic and anaerobic conditions with a correlation coefficient of 0.92 ( p < 0.05), as experimentally observed [25, 37, 38, 41, 42, 47]. …”

Section: Resultssupporting

confidence: 79%

Modeling and simulation of the redox regulation of the metabolism in Escherichia coli at different oxygen concentrations

Matsuoka

Kurata

2017

Biotechnol Biofuels

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BackgroundMicrobial production of biofuels and biochemicals from renewable feedstocks has received considerable recent attention from environmental protection and energy production perspectives. Many biofuels and biochemicals are produced by fermentation under oxygen-limited conditions following initiation of aerobic cultivation to enhance the cell growth rate. Thus, it is of significant interest to investigate the effect of dissolved oxygen concentration on redox regulation in Escherichia coli, a particularly popular cellular factory due to its high growth rate and well-characterized physiology. For this, the systems biology approach such as modeling is powerful for the analysis of the metabolism and for the design of microbial cellular factories.ResultsHere, we developed a kinetic model that describes the dynamics of fermentation by taking into account transcription factors such as ArcA/B and Fnr, respiratory chain reactions and fermentative pathways, and catabolite regulation. The hallmark of the kinetic model is its ability to predict the dynamics of metabolism at different dissolved oxygen levels and facilitate the rational design of cultivation methods. The kinetic model was verified based on the experimental data for a wild-type E. coli strain. The model reasonably predicted the metabolic characteristics and molecular mechanisms of fnr and arcA gene-knockout mutants. Moreover, an aerobic–microaerobic dual-phase cultivation method for lactate production in a pfl-knockout mutant exhibited promising yield and productivity.ConclusionsIt is quite important to understand metabolic regulation mechanisms from both scientific and engineering points of view. In particular, redox regulation in response to oxygen limitation is critically important in the practical production of biofuel and biochemical compounds. The developed model can thus be used as a platform for designing microbial factories to produce a variety of biofuels and biochemicals.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-017-0867-0) contains supplementary material, which is available to authorized users.

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Section: Resultssupporting

confidence: 79%

Modeling and simulation of the redox regulation of the metabolism in Escherichia coli at different oxygen concentrations

Matsuoka

Kurata

2017

Biotechnol Biofuels

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“…It has been reported that an sdhB mutant lacking succinate dehydrogenase colonized as well as its wild type parent (39). However, E. coli has a second isoform of succinate dehydrogenase: fumarate reductase, which provides redundant enzyme function under some circumstances (49). Indeed, an E. coli sdhAB frdA double mutant has a significant colonization defect (Table 1).…”

Section: Central Metabolism and Intestinal Colonizationmentioning

confidence: 99%

Commensal and Pathogenic Escherichia coli Metabolism in the Gut

2015

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E. coli is a ubiquitous member of the intestinal microbiome. This organism resides in a biofilm comprised of a complex microbial community within the mucus layer where it must compete for the limiting nutrients that it needs to grow fast enough to stably colonize. In this article we discuss the nutritional basis of intestinal colonization. Beginning with basic ecological principles we describe what is known about the metabolism that makes E. coli such a remarkably successful member of the intestinal microbiota. To obtain the simple sugars and amino acids that it requires, E. coli depends on degradation of complex glycoproteins by strict anaerobes. Despite having essentially the same core genome and hence the same metabolism when grown in the laboratory, different E. coli strains display considerable catabolic diversity when colonized in mice. To explain why some E. coli mutants do not grow as well on mucus in vitro as their wild type parents yet are better colonizers, we postulate that each one resides in a distinct “Restaurant” where it is served different nutrients because it interacts physically and metabolically with different species of anaerobes. Since enteric pathogens that fail to compete successfully for nutrients cannot colonize, a basic understanding of the nutritional basis of intestinal colonization will inform efforts to develop prebiotics and probiotics to combat infection.

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“…This allows an aerobiosis scale to be defined with 100% aerobiosis being the minimal oxygen concentration needed to suppress acetate formation and 0% aerobiosis being fully anaerobic conditions, where the specific rate of acetate formation is maximal. The wild-type MG1655 and specific metabolic mutant strains were already analyzed over the aerobiosis scale [4]; amongst others, increasing aerobiosis alters the expression of genes encoding respiratory enzymes. There are two NADH-quinone oxidoreductases in the respiratory chain of E. coli [5].…”

Section: Introductionmentioning

confidence: 99%

“…NADH dehydrogenase I (NDH-1, encoded in the nuo -operon) is a proton-pump [6], [7] while NADH dehydrogenase II (NDH-2, encoded by ndh ) is not [5]. In glucose-limited continuous cultures expression of nuoN (indicative of NADH dehydrogenase I) increases gradually from 0% to 100% aerobiosis, whilst expression of ndh is maximal under anaerobic and low microaerobic conditions [4]. The main electron flux in aerobic, glucose-limited chemostats is mediated by NADH dehydrogenase I [6], the distribution of flux between the alternative dehydrogenases is affected by the growth rate.…”

Section: Introductionmentioning

confidence: 99%

“…While all three contribute to generate a proton-motive force, only cytochrome bo (Cyt bo) functions as a true proton pump [13], [14]. It has a relatively low affinity for oxygen [15], [16] and functions therefore mainly under aerobic conditions, where its expression is maximal [15], [17] [4]. The main respiratory activity in the microaerobic range is linked to cytochrome bd -I (Cyt bd-I ) [3], which has a higher affinity for oxygen [13], [15], [18], [19] and is maximally expressed in the microaerobic range [17], [20] between 50 and 100% aerobiosis [4].…”

Section: Introductionmentioning

confidence: 99%

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Analysis of Escherichia coli Mutants with a Linear Respiratory Chain

2014

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The respiratory chain of E. coli is branched to allow the cells' flexibility to deal with changing environmental conditions. It consists of the NADH:ubiquinone oxidoreductases NADH dehydrogenase I and II, as well as of three terminal oxidases. They differ with respect to energetic efficiency (proton translocation) and their affinity to the different quinone/quinol species and oxygen. In order to analyze the advantages of the branched electron transport chain over a linear one and to assess how usage of the different terminal oxidases determines growth behavior at varying oxygen concentrations, a set of isogenic mutant strains was created, which lack NADH dehydrogenase I as well as two of the terminal oxidases, resulting in strains with a linear respiratory chain. These strains were analyzed in glucose-limited chemostat experiments with defined oxygen supply, adjusting aerobic, anaerobic and different microaerobic conditions. In contrast to the wild-type strain MG1655, the mutant strains produced acetate even under aerobic conditions. Strain TBE032, lacking NADH dehydrogenase I and expressing cytochrome bd-II as sole terminal oxidase, showed the highest acetate formation rate under aerobic conditions. This supports the idea that cytochrome bd-II terminal oxidase is not able to catalyze the efficient oxidation of the quinol pool at higher oxygen conditions, but is functioning mainly under limiting oxygen conditions. Phosphorylation of ArcA, the regulator of the two-component system ArcBA, besides Fnr the main transcription factor for the response towards different oxygen concentrations, was studied. Its phosphorylation pattern was changed in the mutant strains. Dephosphorylation and therefore inactivation of ArcA started at lower aerobiosis levels than in the wild-type strain. Notably, not only the micro- and aerobic metabolism was affected by the mutations, but also the anaerobic metabolism, where the respiratory chain should not be important.

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Characterization of E. coli MG1655 and frdA and sdhC mutants at various aerobiosis levels

Cited by 33 publications

References 58 publications

Modeling and simulation of the redox regulation of the metabolism in Escherichia coli at different oxygen concentrations

Modeling and simulation of the redox regulation of the metabolism in Escherichia coli at different oxygen concentrations

Commensal and Pathogenic Escherichia coli Metabolism in the Gut

Analysis of Escherichia coli Mutants with a Linear Respiratory Chain

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