A systematic analysis of TCA Escherichia coli mutants reveals suitable genetic backgrounds for enhanced hydrogen and ethanol production using glycerol as main carbon source

Metabolomics of Escherichia coli for Disclosing Novel Metabolic Engineering Strategies for Enhancing Hydrogen and Ethanol Production

The biological production of hydrogen is an appealing approach to mitigating the environmental problems caused by the diminishing supply of fossil fuels and the need for greener energy. Escherichia coli is one of the best-characterized microorganisms capable of consuming glycerol-a waste product of the biodiesel industry-and producing H₂ and ethanol. However, the natural capacity of E. coli to generate these compounds is insufficient for commercial or industrial purposes. Metabolic engineering allows for the rewiring of the carbon source towards H₂ production, although the strategies for achieving this aim are difficult to foresee. In this work, we use metabolomics platforms through GC-MS and FT-IR techniques to detect metabolic bottlenecks in the engineered ΔldhΔgndΔfrdBC::kan (M4) and ΔldhΔgndΔfrdBCΔtdcE::kan (M5) E. coli strains, previously reported as improved H₂ and ethanol producers. In the M5 strain, increased intracellular citrate and malate were detected by GC-MS. These metabolites can be redirected towards acetyl-CoA and formate by the overexpression of the citrate lyase (CIT) enzyme and by co-overexpressing the anaplerotic human phosphoenol pyruvate carboxykinase (hPEPCK) or malic (MaeA) enzymes using inducible promoter vectors. These strategies enhanced specific H₂ production by up to 1.25- and 1.49-fold, respectively, compared to the reference strains. Other parameters, such as ethanol and H₂ yields, were also enhanced. However, these vectors may provoke metabolic burden in anaerobic conditions. Therefore, alternative strategies for a tighter control of protein expression should be addressed in order to avoid undesirable effects in the metabolic network.

Fatty acid feedstocks enable a highly efficient glyoxylate-TCA cycle for high-yield production of β-alanine

Metabolic engineering to produce tricarboxylic acid (TCA) cycle-derived chemicals is usually associated with problems of low production yield and impaired cellular metabolism. In this work, we found that fatty acid (FA) feedstocks could enable high-yield production of TCA cycle-derived chemicals, while maintaining an efficient and balanced metabolic flux of the glyoxylate-TCA cycle, which is favorable for both product synthesis and cell growth. Here, we designed a novel synthetic pathway for production of β-alanine, an important TCA cycle-derived product, from FAs with a high theortecial yield of 1.391 g/g. By introducing panD, improving aspA, and knocking out iclR, glyoxylate shunt was highly activated in FAs and the yield of β-alanine reached 0.71 g/g from FAs, much higher than from glucose. Blocking the TCA cycle at icd/sucA/fumAC nodes could increase β-alanine yield in a flask cultivation, but severely reduced cell growth and FA utilization during fed-batch processes. Replenishing oxaloacetate by knocking out aspC and recovering fumAC could restore the growth and lead to a titer of 35.57 g/l. After relieving the oxidative stress caused by FA metabolism, β-alanine production could reach 72.05 g/l with a maximum yield of 1.24 g/g, about 86% of the theoretical yield. Our study thus provides a promising strategy for the production of TCA cycle-derived chemicals.

Escherichia coli Dcu C4-dicarboxylate transporters dependent proton and potassium fluxes and FOF1-ATPase activity during glucose fermentation at pH 7.5

During fermentation in Escherichia coli succinate is transported via Dcu transporters, encoded dcuA, dcuB, dcuC and dcuD although the role of DcuD protein has not been elucidated yet. It has been shown contribution of Dcu transporters in the N,N'-dicyclohexylcarbodiimide (DCCD) sensitive proton and potassium transport through the cytoplasmic membrane and membrane-associated ATPase activity. Total H^± efflux was decreased ~ 40% while K^± uptake was absent in dcuD mutant. DCCD-sensitive H^± flux was absent in dcuD nevertheless it was increased ~ 3 fold in dcuACB. K^± uptake in dcuACB was stimulated ~ 30% compared to wild type but in DCCD assays K^± ions were effluxed with the rate of 0.15 mmol/min per 10⁹ cells/ml. In dcuACB mutant membrane potential (ΔΨ) was ~ 30 mV higher than in wild type. dcuD gene expression was increased in the dcuACB mutant respect to wild type at pH 7.5 (~120%), suggesting that an increment of DcuD activity compensates the lack of DcuA, DcuC and DcuB carriers. It can be concluded that active DcuD is important for H^± efflux via the F_OF₁-ATPase and K^± uptake at pH 7.5. In addition, DcuA, DcuB and DcuC transporters are crucial for regulating DCCD-sensitive K^± transport and ΔΨ in E. coli.

Evidence for Escherichia coli DcuD carrier dependent FOF1-ATPase activity during fermentation of glycerol

During fermentation Escherichia coli excrete succinate mainly via Dcu family carriers. Current work reveals the total and N,N'-dicyclohexylcarbodiimide (DCCD) inhibited ATPase activity at pH 7.5 and 5.5 in E. coli wild type and dcu mutants upon glycerol fermentation. The overall ATPase activity was highest at pH 7.5 in dcuABCD mutant. In wild type cells 50% of the activity came from the FOF1-ATPase but in dcuD mutant it reached ~80%. K+ (100 mM) stimulate total but not DCCD inhibited ATPase activity 40% and 20% in wild type and dcuD mutant, respectively. 90% of overall ATPase activity was inhibited by DCCD at pH 5.5 only in dcuABC mutant. At pH 7.5 the H+ fluxes in E. coli wild type, dcuD and dcuABCD mutants was similar but in dcuABC triple mutant the H+ flux decreased 1.4 fold reaching 1.15 mM/min when glycerol was supplemented. In succinate assays the H+ flux was higher in the strains where DcuD is absent. No significant differences were determined in wild type and mutants specific growth rate except dcuD strain. Taken together it is suggested that during glycerol fermentation DcuD has impact on H+ fluxes, FOF1-ATPase activity and depends on potassium ions.

Heterologous expression of the human Phosphoenol Pyruvate Carboxykinase (hPEPCK-M) improves hydrogen and ethanol synthesis in the Escherichia coli dcuD mutant when grown in a glycerol-based medium

The production of biodiesel has emerged as an alternative to fossil fuels. However, this industry generates glycerol as a by-product in such large quantities that it has become an environmental problem. The biotransformation of this excess glycerol into other renewable bio-energy sources, like H₂ and ethanol, by microorganisms such as Escherichia coli is an interesting possibility that warrants investigation. In this work we hypothesized that the conversion of oxaloacetate (OAA) to phosphoenolpyruvate (PEP) could be improved by a controlled expression of the human mitochondrial GTP-dependent PEP carboxykinase. This heterologous expression was tested in several E. coli mutant backgrounds with increased availability of C4 intermediates. It was found that this metabolic rewiring improved the synthesis of the target products in several mutants, with the dcuD mutant being the most suitable background for hydrogen and ethanol specific productions and glycerol consumption. These factors increased by 2.46, 1.73 and 1.95 times, respectively, when compared to those obtained for the wild-type strain.

Editorial: Biotechnology Journal brings more than biotechnology

Biotechnology Journal always brings the state-of-the-art biotechnologies to our readers. Different from other topical issues, this issue of Biotechnology Journal is complied with a series of exiting reviews and research articles from spontaneous submissions, again, addressing society's actual problems and needs. The progress is a real testimony how biotechnology contributes to achievements in healthcare, better utilization of resources, and a bio-based economy.

Improved glycerol to ethanol conversion by E. coli using a metagenomic fragment isolated from an anaerobic reactor

Crude glycerol obtained as a by-product of biodiesel production is a reliable feedstock with the potential to be converted into reduced chemicals with high yields. It has been previously shown that ethanol is the primary product of glycerol fermentation by Escherichia coli. However, few efforts were made to enhance this conversion by means of the expression of heterologous genes with the potential to improve glycerol transport or metabolism. In this study, a fosmid-based metagenomic library constructed from an anaerobic reactor purge sludge was screened for genetic elements that promote the use and fermentation of crude glycerol by E. coli. One clone was selected based on its improved growth rate on this feedstock. The corresponding fosmid, named G1, was fully sequenced (41 kbp long) and the gene responsible for the observed phenotype was pinpointed by in vitro insertion mutagenesis. Ethanol production from both pure and crude glycerol was evaluated using the parental G1 clone harboring the ethanologenic plasmid pLOI297 or the industrial strain LY180 complemented with G1. In mineral salts media containing 50 % (v/v) pure glycerol, ethanol concentrations increased two-fold on average when G1 was present in the cells reaching up to 20 g/L after 24 h fermentation. Similar fermentation experiments were done using crude instead of pure glycerol. With an initial OD620 of 8.0, final ethanol concentrations after 24 h were much higher reaching 67 and 75 g/L with LY180 cells carrying the control fosmid or the G1 fosmid, respectively. This translates into a specific ethanol production rate of 0.39 g h−1 OD−1 L−1.

Toward glycerol biorefinery: metabolic engineering for the production of biofuels and chemicals from glycerol

As an inevitable by-product of the biofuel industry, glycerol is becoming an attractive feedstock for biorefinery due to its abundance, low price and high degree of reduction. Converting crude glycerol into value-added products is important to increase the economic viability of the biofuel industry. Metabolic engineering of industrial strains to improve its performance and to enlarge the product spectrum of glycerol biotransformation process is highly important toward glycerol biorefinery. This review focuses on recent metabolic engineering efforts as well as challenges involved in the utilization of glycerol as feedstock for the production of fuels and chemicals, especially for the production of diols, organic acids and biofuels.