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PubMedDate not supplied

High cell density culture of metabolically engineered Escherichia coli for the production of poly(3-hydroxybutyrate) in a defined medium.

A recombinant Escherichia coli strain XL1-Blue harboring a stable high-copy-number plasmid pSYL107 containing the Alcaligenes eutrophus polyhydroxyalkanoate biosynthesis genes and the Escherichia coli ftsZ gene was employed for the production of poly(3-hydroxybutyrate) (PHB) by fed-batch culture in a defined medium. Suppression of filamentation by overexpressing the cell division protein FtsZ allowed production of PHB to a high concentration (77 g/L) with high productivity (2 g/L/h) in a defined medium, which was not possible with the recombinant E. coli that underwent filamentation. Further optimization of fed-batch culture condition resulted in PHB concentration of 104 g/L in a defined medium, which was the highest value reported to date by employing recombinant E. coli.

Alcaligenes↗
PubMed2004

Biosynthesis of R-3-hydroxyalkanoic acids by metabolically engineered Escherichia coli.

An efficient system for the production of (R)-hydroxyalkanoic acids (RHAs) was developed in natural polyhydroxyalkanoate (PHA)-producing bacteria and recombinant Escherichia coli. Acidic alcoholysis of purified PHA and in vivo depolymerization of PHA accumulated in the cells allowed the production of RHAs. In recombinant E. coli, RHA production was achieved by removing CoA from (R)-3-hydroxyacyl-CoA and by in vivo depolymerization of PHA. When the recombinant E. coli harboring the Ralstonia eutropha PHA biosynthesis genes and the depolymerase gene was cultured in a complex or a chemically defined medium containing glucose, (R)-3-hydroxybutyric acid (R3HB) was produced as monomers and dimers. R3HB dimers could be efficiently converted to monomers by mild alkaline heat treatment. A stable recombinant E. coli strain in which the R. eutropha PHA biosynthesis genes were integrated into the chromosome disrupting the pta gene was constructed and examined for the production of R3HB. When the R. eutropha intracellular depolymerase gene was expressed by using a stable plasmid containing the hok/sok locus of plasmid R1, R3HB could be efficiently produced.

Alcohols↗
PubMed2003

Metabolic engineering of Escherichia coli: construction of an efficient biocatalyst for D-mannitol formation in a whole-cell biotransformation.

A whole-cell biotransformation system for the conversion of D-fructose to D-mannitol was developed in Escherichia coli by construction of a recombinant oxidation/reduction cycle. First, the mdh gene encoding for the mannitol dehydrogenase of Leuconostoc pseudomesenteroides ATCC 12291 (MDH) was expressed, effecting a strong catalytic activity of a NADH-dependent reduction of D-fructose to D-mannitol in cell extracts of the recombinant E. coli strain but not enabling whole cells of the strain to produce D-mannitol from D-fructose. To provide a source for reduction equivalents needed for D-fructose reduction, the fdh gene from Mycobacterium vaccae N10 (FDH) encoding formate dehydrogenase was functionally co-expressed. FDH generates NADH used for D-fructose reduction by dehydrogenation of formate to carbon dioxide. These recombinant E. coli cells were able to form D-mannitol from D-fructose in a low but significant quantity (15 mM). The introduction of a further gene, encoding for the glucose facilitator protein of Zymomonas mobilis (GLF) enabled the cells to efficiently take up D-fructose into the cells, without simultaneous phosphorylation. Resting cells of this E. coli strain (3 g cell dry weight/l) produced 216 mM D-mannitol in 17 hours. Biotransformations conducted under pH-control by formic acid addition yielded D-mannitol at a concentration of 362 mM within 8 hours. The yield Y(D-mannitol D-fructose) was 84 [mol%]. These results show that the recombinant strain of E. coli can be utilized as an efficient biocatalyst for D-mannitol formation.

Biotransformation↗
PubMed2004

[Plant volatiles and their metabolic engineering].

Plant volatiles mainly include terpenoid, benzenoid/phenylpropanoid and fatty-acid derivatives, and they play diverse roles in plant-plant and plant-insect communications. In recent years, great progress has been made in biochemical and molecular characterization of the formation and release of these volatiles, and this make it possible to dissect their biological functions. More than 30 kinds of genes related with biosynthesis of these volatiles have been cloned. The pathways leading to synthesis of these metabolites can be controlled by enzyme activity and the substrates available as well as gene architecture. Plant volatiles can serve as attractants for specific pollinators, important cellular regulators in developmental processes and protection against environmental stress, whereas those released after herbivory or pathogen attacks can induce the expression a set of defensive genes or attraction of predators of the herbivores. An attractive prospect in this area is to design scent spectrum of plant with genetic and molecular technology. Two alternative approaches are used to genetically engineer these plant volatiles. One is based on the introduction of foreign genes encoding enzymes with activities that are missing in target plant, while the other is focused on modulating the expression of native genes.

Cloning, Molecular↗
PubMed2001

Metabolic engineering of Escherichia coli: construction and characterization of a gltA (citrate synthase) knockout mutant.

E. coli is one of the most important host organisms for recombinant protein production. However, growth and recombinant protein production can be limited by acetate accumulation during high-cell-density fermentations. Some of the strategies used to overcome this problem are based on the alteration of the genotype of the host. This paper discusses the construction and characterization of an E. coli gltA- knockout mutant. The knockout of the gene was confirmed by the loss of citrate synthase activity in an enzyme assay. Also the growth rate of the mutant on Luria Broth and Luria Broth + acetate was reduced.

Citrate (si)-Synthase↗
PubMed2000

Metabolic engineering study on the direct fermentation of 2-keto-L-gulonic acid, a key intermediate of L-ascorbic acid in Pseudomonas putida IFO3738.

We have achieved production of 2-keto-L-gulonic acid (2-KLGA) in recombinant Pseudomonas putida IFO3738. Firstly, the genes for sorbose dehydrogenase (SDH)/sorbosone dehydrogenase (SNDH) were introduced into P. putida. The recombinant P. putida/pBBR-SDH produced 0.7 mg/ml of 2-KLGA in a culture broth containing 5% L-sorbose. Replacement of the native SNDH promoter by the Escherichia coli tufB promoter (pBBR-SDH-tufB) improved the productivity of 2-KLGA up to 11.4 mg/ml. Secondly, the sorbitol dehydrogenase (SLDH) gene was also introduced into P. putida. The recombinant P. putida/pUCP19-3DH carrying the genes for SDH, SNDH and SLDH had the ability to produce 2-KLGA (7.5 mg/ml) in a 5% d-sorbitol broth. The productivity of 2-KLGA was improved up to 9.8 mg/ml by changing to an expression system with two plasmids, pBBR-SDH-tufB (for SDH/SNDH) and pUCP19-SLDH (for SLDH), respectively. Moreover, the replacement of the native SLDH promoter by the E. coli tufB promoter (pUCP19-SLDH-tufB) improved the 2-KLGA productivity up to 11.6 mg/ml. Optimization of cultivation conditions increased the conversion yield of 2-KLGA to 32% and that of l-idonate, a metabolite of 2-KLGA, to 40%. These results indicate P. putida IFO3738 is one of the candidate strains for direct fermentation of 2-KLGA.

Journal Article↗
PubMed2003

Engineering central metabolism in crop species: learning the system.

Over many centuries much effort has been expended on crop improvement, most recently by use of molecular genetic technologies. Although genome sequence information for crop species is not yet available in the public domain, most of the genes of central metabolism have already been cloned and the corresponding transgenic plants generated. Although these plants have often confirmed the hypotheses based on more indirect methodologies, they have also produced unexpected challenges to the metabolic engineer in outlining the enormous flexibility and complexity inherent in plant metabolism. Intriguingly, comparison of transcript and metabolite levels of the TCA cycle revealed strong correlations in expression levels but little coordination in the levels of metabolic intermediates. These factors explain why many attempts to engineer central metabolism have proven unsuccessful to date and suggest that a greater understanding of the regulatory circuits and networks controlling metabolism is required before engineering can become routine. In this article we intend to illustrate these challenges by reviewing attempts to manipulate the central metabolic pathways of Solanaceae (sps.) as well as demonstrating the role for systems biology approaches in metabolic engineering in crops.

Agriculture↗
PubMed2025

Engineering of xylose metabolic pathways in Rhodotorula toruloides for sustainable biomanufacturing.

The oleaginous yeast Rhodotorula toruloides is a promising microbial cell factory for the sustainable production of biofuels and value-added chemicals from renewable carbon sources. Unlike the conventional yeast Saccharomyces cerevisiae, R. toruloides can naturally metabolize xylose, the second most abundant sugar in lignocellulosic hydrolysates. However, its native xylose metabolism is inefficient, characterized by slow xylose uptake and accumulation of D-arabitol. Moreover, despite its phenotype, research on the enzymes involved in xylose metabolism has yet to reach a consensus. Therefore, this review provides a comprehensive analysis of the non-canonical xylose metabolism in R. toruloides, focusing on the properties of key enzymes involved in xylose metabolism. Native xylose reductase and xylitol dehydrogenase exhibit broad substrate promiscuity compared to their counterparts in the xylose-fermenting Scheffersomyces stipitis. Additionally, the absence of xylulokinase expression under xylose-utilizing conditions redirects metabolism toward D-arabitol accumulation. Consequently, D-arabitol dehydrogenases and ribulokinase play essential roles in the xylose metabolism of R. toruloides. These findings highlight the fundamental differences between R. toruloides xylose metabolism and the oxidoreductase pathways observed in other xylose-fermenting yeast, providing insights for metabolic engineering strategies to improve xylose utilization and enhance bioconversion of cellulosic hydrolysates to different bioproducts by R. toruloides.

Xylose↗
PubMed1999

Nonlinear metabolic control analysis.

Mathematical description of metabolic systems allows the calculation of the expected responses of metabolism to genetic modifications and the identification of the most promising targets for metabolic engineering. Metabolic control analysis (MCA) provides such a description in the form of quantitative indices (elasticities and control coefficients). These indices are determined by perturbation experiments around a reference steady state and, therefore, the predictive power of MCA is limited to small changes in the metabolic parameters. The modeling framework introduced here allows accurate description of the metabolic responses over wide range of changes in the metabolic parameters. The framework requires information about the MCA indices at the reference state and the corresponding values of the metabolic reaction rates, and employs simplifying assumptions about the reaction mechanisms. It is shown that knowledge of the intracellular metabolite concentrations is not necessary for the application of the framework. The performance of the methodology is illustrated using three elementary metabolic systems that display highly nonlinear responses to the modification in their parameters: an unbranched pathway, an interconvertible enzyme system, and a branched pathway subject to feedback inhibition.

Metabolism↗
PubMed2006

Genetic engineering of Nicotiana tabacum for reduced nornicotine content.

UNLABELLED: Nornicotine is an undesirable secondary alkaloid in cultivated tobacco, because it serves as a precursor to N'-nitrosonornicotine (NNN), a tobacco-specific nitrosamine with suspected carcinogenic properties. Nornicotine is produced through the oxidative N-demethylation of nicotine by a nicotine N-demethylase enzyme during the senescence and curing of tobacco leaves. While the nornicotine content of most commercial burley tobacco is low, a process termed "conversion" can bestow considerably increased nornicotine levels in a portion of the plants within the population. Previously, we isolated a nicotine N-demethylase gene, designated CYP82E4, and demonstrated that RNAi-induced silencing of CYP82E4 and its close homologues is an effective means for suppressing nicotine to nornicotine conversion. In this study, we used real-time polymerase chain reaction to confirm the central role of CYP82E4 in nicotine N-demethylation by demonstrating that the transcript accumulation of CYP82E4 is enhanced as much as 80-fold in converter vs nonconverter tobacco. We also show the design of an optimized RNAi construct (82E4Ri298) that suppressed nicotine to nornicotine conversion from 98% to as low as 0.8% in a strong converter tobacco line, a rate of nornicotine production that is about 3.6-fold lower than typically detected in commercial varieties. Southern blot analysis showed that a single copy of the RNAi transgene was as effective in suppressing nornicotine accumulation as multiple copies. Greenhouse-grown transgenic plants transformed with the RNAi construct were morphologically indistinguishable from the empty vector or wild-type controls. These results demonstrate that the genetic transformation of tobacco with the 82E4Ri298 construct is an effective strategy for reducing nornicotine and ultimately NNN levels in tobacco. KEYWORDS: Alkaloid; cytochrome P450; gene silencing; nicotine N-demethylase; N'-nitrosonornicotine; plant genetic engineering; metabolic engineering; Nicotiana tabacum L.; real-time PCR; RNA interference; tobacco-specific nitrosamines.

Cytochrome P-450 Enzyme System↗
PubMed2002

MMT--a pathway modeling tool for data from rapid sampling experiments.

The identification of metabolic regulation is a major concern in metabolic engineering. Metabolic regulation phenomena depend on intracellular compounds such as enzymes, metabolites and cofactors. A complete understanding of metabolic regulation requires quantitative information about these compounds under in vivo conditions. This quantitative knowledge in combination with the known network of metabolic pathways allows the construction of mathematical models that describe the dynamic changes in metabolite concentrations over time. Rapid sampling combined with pulse experiments is a useful tool for the identification of metabolic regulation owing to the transient data they provide. Enzymatic tests in combination with ESI-LC-MS (Electrospray Ionization Liquid Chromatographic Tandem Mass Spectrometry) and HPLC measurements have been used to identify up to 30 metabolites and nucleotides from rapid sampling experiments. A metabolic modeling tool (MMT) that is built on a relational database was developed specifically for analysis of rapid sampling experiments. The tool allows to construct complex pathway models with information stored in the relational database. Parameter fitting and simulation algorithms for the resulting system of Ordinary Differential Equations (ODEs) are part of MMT. Additionally explicit sensitivity functions are calculated. The integration of all necessary algorithms in one tool allows fast model analysis and comparison. Complex models have been developed to describe the central metabolic pathways of Escherichia coli during a glucose pulse experiment.

Algorithms↗
PubMed1999

Engineering a central metabolic pathway: glycolysis with no net phosphorylation in an Escherichia coli gap mutant complemented with a plant GapN gene.

A cDNA fragment containing the Pisum sativum GapN gene, which encodes the non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase, was cloned in a prokaryote expression vector. This construct enabled Escherichia coli strain W3CG, a mutant which lacks the glycolytic phosphorylating G3P dehydrogenase, to grow aerobically on sugars. The functionally complemented mutant exhibited high levels of the catalytically active plant enzyme, which renders 3-phosphoglycerate and NADPH, thus bypassing the first substrate level phosphorylation step of the glycolysis. As expected if such a glycolytic bypass would be operative in vivo, this clone failed to grow anaerobically on sugars in contrast to W3CG clones complemented with phosphorylating glyceraldehyde-3-phosphate dehydrogenases. According to the irreversible catabolic character of the non-phosphorylating reaction, the GapN-complemented clone was unable to grow on gluconeogenic substrates. This metabolic engineering approach demonstrates that a pure catabolic Embden-Meyerhof pathway with no net energy yield is feasible.

Escherichia coli↗
PubMed2003

Metabolic pathway engineering in lactic acid bacteria.

Lactic acid bacteria (LAB) display a relatively simple carbon and energy metabolism where the sugar source is converted mainly to lactic acid. In Lactococcus lactis metabolic engineering has been very successful in the re-routing of lactococcal pyruvate metabolism to products other than lactic acid. Current metabolic engineering approaches tend to focus on more complex, biosynthetic pathways leading to end-products that generate a health benefit for the consumer (nutraceuticals). Several examples of research on these minor pathways in L. lactis have illustrated the potential of LAB as producers of these metabolites. Whole genome sequencing efforts and corresponding global technologies will have an impact on metabolic engineering in the future.

Bacterial Proteins↗
PubMed2006

Physiological and genetic engineering of cytosolic redox metabolism in Saccharomyces cerevisiae for improved glycerol production.

Previous metabolic engineering strategies for improving glycerol production by Saccharomyces cerevisiae were constrained to a maximum theoretical glycerol yield of 1 mol.(molglucose)(-1) due to the introduction of rigid carbon, ATP or redox stoichiometries. In the present study, we sought to circumvent these constraints by (i) maintaining flexibility at fructose-1,6-bisphosphatase and triosephosphate isomerase, while (ii) eliminating reactions that compete with glycerol formation for cytosolic NADH and (iii) enabling oxidative catabolism within the mitochondrial matrix. In aerobic, glucose-grown batch cultures a S. cerevisiae strain, in which the pyruvate decarboxylases the external NADH dehydrogenases and the respiratory chain-linked glycerol-3-phosphate dehydrogenase were deleted for this purpose, produced glycerol at a yield of 0.90 mol.(molglucose)(-1). In aerobic glucose-limited chemostat cultures, the glycerol yield was ca. 25% lower, suggesting the involvement of an alternative glucose-sensitive mechanism for oxidation of cytosolic NADH. Nevertheless, in vivo generation of additional cytosolic NADH by co-feeding of formate to aerobic, glucose-limited chemostat cultures increased the glycerol yield on glucose to 1.08 mol mol(-1). To our knowledge, this is the highest glycerol yield reported for S. cerevisiae.

Bioreactors↗