Acetate metabolism regulation in Escherichia coli: carbon overflow, pathogenicity, and beyond

Bernal, Vicente; Castaño-Cerezo, Sara; Cánovas, Manuel

doi:10.1007/s00253-016-7832-x

Cited by 96 publications

(101 citation statements)

References 155 publications

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“…Acetate was the primary product at DO levels >15%. This acetate overflow was observed together with high CO 2 production at a high growth rate in E. coli [45, 46], as shown in Additional file 3: Figure S3. The acetate concentration increased with decrease in the DO level (3–14%), as observed experimentally [24].…”

Section: Resultsmentioning

confidence: 99%

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: Resultsmentioning

confidence: 99%

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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“…In Escherichia coli K12 acetate is a major product of metabolism under both aerobic and anaerobic growth conditions (Figure 1) (Wolfe, 2005;Bernal et al, 2016). Under aerobic conditions at high growth rates, e.g., during batch growth with glucose, acetate is produced by the so-called overflow metabolism.…”

Section: Introductionmentioning

confidence: 99%

The Impact of ackA, pta, and ackA-pta Mutations on Growth, Gene Expression and Protein Acetylation in Escherichia coli K-12

et al. 2020

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Acetate is a characteristic by-product of Escherichia coli K-12 growing in batch cultures with glucose, both under aerobic as well as anaerobic conditions. While the reason underlying aerobic acetate production is still under discussion, during anaerobic growth acetate production is important for ATP generation by substrate level phosphorylation. Under both conditions, acetate is produced by a pathway consisting of the enzyme phosphate acetyltransferase (Pta) producing acetyl-phosphate from acetyl-coenzyme A, and of the enzyme acetate kinase (AckA) producing acetate from acetyl-phosphate, a reaction that is coupled to the production of ATP. Mutants in the AckA-Pta pathway differ from each other in the potential to produce and accumulate acetyl-phosphate. In the publication at hand, we investigated different mutants in the acetate pathway, both under aerobic as well as anaerobic conditions. While under aerobic conditions only small changes in growth rate were observed, all acetate mutants showed severe reduction in growth rate and changes in the by-product pattern during anaerobic growth. The AckA − mutant showed the most severe growth defect. The glucose uptake rate and the ATP concentration were strongly reduced in this strain. This mutant exhibited also changes in gene expression. In this strain, the atoDAEB operon was significantly upregulated under anaerobic conditions hinting to the production of acetoacetate. During anaerobic growth, protein acetylation increased significantly in the ackA mutant. Acetylation of several enzymes of glycolysis and central metabolism, of aspartate carbamoyl transferase, methionine synthase, catalase and of proteins involved in translation was increased. Supplementation of methionine and uracil eliminated the additional growth defect of the ackA mutant. The data show that anaerobic, fermentative growth of mutants in the AckA-Pta pathway is reduced but still possible. Growth reduction can be explained by the lack of an important ATP generating pathway of mixed acid fermentation. An ackA deletion mutant is more severely impaired than pta or ackA-pta deletion mutants. This is most probably due to the production of acetyl-P in the ackA mutant, leading to increased protein acetylation.

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“…60 Overflow metabolism was also evaluated by measuring the specific rate of acetate formation (Table 3), since this metabolite is known to be the main byproduct of aerobic glucose catabolism. 61 E. coli BW25113 carrying pSEVA224 excreted acetate at a rate of 4.8 ± 0.2 mmol g CDW –1 h –1 when cultured in LB medium containing glucose. All the strains expressing the phaC1AB1 gene cluster had a reduced rate of acetate formation ( e.g.…”

Section: Resultsmentioning

confidence: 99%

Refactoring the Embden–Meyerhof–Parnas Pathway as a Whole of Portable GlucoBricks for Implantation of Glycolytic Modules in Gram-Negative Bacteria

2017

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The Embden–Meyerhof–Parnas (EMP) pathway is generally considered to be the biochemical standard for glucose catabolism. Alas, its native genomic organization and the control of gene expression in Escherichia coli are both very intricate, which limits the portability of the EMP pathway to other biotechnologically important bacterial hosts that lack the route. In this work, the genes encoding all the enzymes of the linear EMP route have been individually recruited from the genome of E. coli K-12, edited in silico to remove their endogenous regulatory signals, and synthesized de novo following a standard (GlucoBrick) that enables their grouping in the form of functional modules at the user’s will. After verifying their activity in several glycolytic mutants of E. coli, the versatility of these GlucoBricks was demonstrated in quantitative physiology tests and biochemical assays carried out in Pseudomonas putida KT2440 and P. aeruginosa PAO1 as the heterologous hosts. Specific configurations of GlucoBricks were also adopted to streamline the downward circulation of carbon from hexoses to pyruvate in E. coli recombinants, thereby resulting in a 3-fold increase of poly(3-hydroxybutyrate) synthesis from glucose. Refactoring whole metabolic blocks in the fashion described in this work thus eases the engineering of biochemical processes where the optimization of carbon traffic is facilitated by the operation of the EMP pathway—which yields more ATP than other glycolytic routes such as the Entner–Doudoroff pathway.

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Acetate metabolism regulation in Escherichia coli: carbon overflow, pathogenicity, and beyond

Cited by 96 publications

References 155 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

The Impact of ackA, pta, and ackA-pta Mutations on Growth, Gene Expression and Protein Acetylation in Escherichia coli K-12

Refactoring the Embden–Meyerhof–Parnas Pathway as a Whole of Portable GlucoBricks for Implantation of Glycolytic Modules in Gram-Negative Bacteria

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