Pathway engineering of Escherichia coli for α-ketoglutaric acid production

Advancements in metabolic engineering: unlocking the potential of key organic acids for sustainable industrial applications

This review explores the advancements, application potential, and challenges of microbial metabolic engineering strategies for sustainable organic acid production. By integrating gene editing, pathway reconstruction, and dynamic regulation, microbial platforms have achieved enhanced biosynthesis of key organic acids such as pyruvate, lactic acid, and succinic acid. Strategies including by-product pathway knockout, key enzyme overexpression, and improved CO2 fixation have contributed to higher production efficiency. Additionally, utilizing non-food biomass sources, such as lignocellulose, algal feedstocks, and industrial waste, has reduced reliance on conventional carbon sources, supporting sustainability goals. However, challenges remain in substrate inhibition, purification complexity, and metabolic flux imbalances. Addressing these requires omics-driven metabolic optimization, stress-resistant strain development, and biorefinery integration. Future research should focus on system-level design to enhance cost-effectiveness and sustainability, advancing industrial bio-manufacturing of organic acids.

Sustainable synthesis of α-ketoglutaric and methanetriacetic acids from biomass feedstocks

α-Ketoglutaric acid (KGA) and methanetriacetic acid (MTA) are important multi-functional carboxylic acids with versatile applications. However, their synthetic processes are still not green and efficient. Herein, we report a novel one-pot approach for sustainable synthesis of KGA and MTA from biomass-derived pyruvic and glyoxylic acids under mild conditions. KGA is synthesized via cross-aldol condensation of pyruvic and glyoxylic acids to 2-hydroxy-4-oxopentanedioic acid, followed by its sequential dehydration and hydrogenation on Pd/TiO2, affording a high yield of 85.4% on a molar basis of glyoxylic acid at 110 °C and 1.0 MPa H2. The synthesis of MTA involves cross-aldol condensation of KGA and glyoxylic acid to 3-(carboxymethyl)-2-hydroxy-4-oxopentanedioic acid and its subsequent hydrodeoxygenation on Pd/TiO2 and MoOx/TiO2 in a high yield of 86.2% at 200 °C and 2.0 MPa H2. This novel approach provides a rationale for the sustainable production of various multi-functional carboxylic acids that are still not easily available.

Metabolically Modifying the Central and Competitive Metabolic Pathways for Enhanced D-Pantoic Acid Synthesis

D-Pantoic acid is an essential precursor for the synthesis of vitamin B5. However, the microbial synthesis of D-pantoic acid suffers from a low yield. Herein, to improve D-pantoic acid biosynthesis in Escherichia coli, the central metabolic and byproduct-forming pathways were first engineered, increasing the D-pantoic acid titer to 1.55 g/L from 0.75 g/L. Subsequently, the modification was focused on preventing the accumulation of α-ketoglutarate (α-KG). Six genes (ppc, mdh, icd, sucA, kgtP, and dcuA) related to α-KG metabolism and transport were screened by the CRISPRi system and further genetically manipulated. Ultimately, significantly improved D-pantoic acid biosynthesis (2.03 g/L in a shake flask and 14.78 g/L in a 5-L bioreactor) with dramatically reduced formation of byproducts was achieved. To our best knowledge, this is the first attempt to modify the key metabolic targets related to α-KG accumulation for enhanced D-pantoic acid biosynthesis. These findings would also offer valuable insights into the metabolic regulation of other related metabolites.

A new-to-nature photosynthesis system enhances utilization of one-carbon substrates in Escherichia coli

Photosynthesis harvests solar energy to convert CO2 into chemicals, offering a potential solution to reduce atmospheric CO2. However, integrating photosynthesis into non-photosynthetic microbes to utilize one-carbon substrates is challenging. Here, a photosynthesis system is reconstructed in E. coli, by integrating light and dark reaction to synthesize bioproducts from one-carbon substrates. A light reaction is reconstructed using the photosystem of photosynthetic bacteria, increasing ATP and NADH contents by 337.9% and 383.7%, respectively. A dark reaction is constructed by designing CO2 fixation pathway to synthesize pyruvate. By assembling the light and dark reaction, a photosynthesis system is established and further programmed by installing an energy adapter, enabling the production of acetone, malate, and α-ketoglutarate, with a negative carbon footprint of -0.84 ~ -0.23 kgCO2e/kg product. Furthermore, light-driven one-carbon trophic growth of E. coli is achieved with a doubling time of 19.86 h. This photosynthesis system provides a green and sustainable approach to enhance one-carbon substrates utilization in the future.

From molasses to purified α-ketoglutarate with engineered Corynebacterium glutamicum

α-ketoglutarate (AKG) is a valuable dicarboxylic acid with multiple applications in the food, pharmaceutical, and chemical industries. Its chemical synthesis is associated with toxic by-products, low specificity, and high energy input. To create a more environmentally friendly and sustainable alternative, a microbial production process for AKG was developed. Four potential producer strains were generated by metabolic engineering of Corynebacteriumglutamicum and characterized on defined glucose/sucrose media as well as molasses, a side stream from sugar beet processing. While strain C.glutamicum PO6-iolT1Δgdh ΔgltB mscCG' ΔodhA was not able to grow on defined media it outperformed all predecessor variants on molasses. Successful scale-up into a fed-batch bioreactor process with molasses yielded 96.2g AKG with a conversion yield of 0.64gg-1. Finally, downstream processing by liquid-liquid extraction with ethyl acetate enabled product purification with an extraction efficiency of 87 % and an AKG purity of > 93 %.

Biotransformation of ethylene glycol by engineered Escherichia coli

There has been extensive research on the biological recycling of PET waste to address the issue of plastic waste pollution, with ethylene glycol (EG) being one of the main components recovered from this process. Therefore, finding ways to convert PET monomer EG into high-value products is crucial for effective PET waste recycling. In this study, we successfully engineered Escherichia coli to utilize EG and produce glycolic acid (GA), expecting to facilitate the biological recycling of PET waste. The engineered E. coli, able to utilize 10 g/L EG to produce 1.38 g/L GA within 96 h, was initially constructed. Subsequently, strategies based on overexpression of key enzymes and knock-out of the competing pathways are employed to enhance EG utilization along with GA biosynthesis. An engineered E. coli, characterized by the highest GA production titer and substrate conversion rate, was obtained. The GA titer increased to 5.1 g/L with a yield of 0.75 g/g EG, which is the highest level in the shake flake experiments. Transcriptional level analysis and metabolomic analysis were then conducted, revealing that overexpression of key enzymes and knock-out of the competing pathways improved the metabolic flow in the EG utilization. The improved metabolic flow also leads to accelerated synthesis and metabolism of amino acids.

Multi-Omics Study on Molecular Mechanisms of Single-Atom Fe-Doped Two-Dimensional Conjugated Phthalocyanine Framework for Photocatalytic Antibacterial Performance

Currently, photocatalysis of the two-dimensional (2D) conjugated phthalocyanine framework with a single Fe atom (CPF-Fe) has shown efficient photocatalytic activities for the removal of harmful effluents and antibacterial activity. Their photocatalytic mechanisms are dependent on the redox reaction-which is led by the active species generated from the photocatalytic process. Nevertheless, the molecular mechanism of CPF-Fe antimicrobial activity has not been sufficiently explored. In this study, we successfully synthesized CPF-Fe with great broad-spectrum antibacterial properties under visible light and used it as an antibacterial agent. The molecular mechanism of CPF-Fe against Escherichia coli and Salmonella enteritidis was explored through multi-omics analyses (transcriptomics and metabolomics correlation analyses). The results showed that CPF-Fe not only led to the oxidative stress of bacteria by generating large amounts of h+ and ROS but also caused failure in the synthesis of bacterial cell wall components as well as an osmotic pressure imbalance by disrupting glycolysis, oxidative phosphorylation, and TCA cycle pathways. More surprisingly, CPF-Fe could disrupt the metabolism of amino acids and nucleic acids, as well as inhibit their energy metabolism, resulting in the death of bacterial cells. The research further revealed the antibacterial mechanism of CPF-Fe from a molecular perspective, providing a theoretical basis for the application of CPF-Fe photocatalytic antibacterial nanomaterials.

Efficient production of α-ketoglutaric acid using an economical double-strain cultivation and catalysis system

The whole-cell catalysis strategy of alpha-ketoglutaric acid (α-KG) production from L-glutamic acid (L-Glu) using recombinant Escherichia coli, in which L-glutamate oxidase (LGox) was over-expressed, has replaced the traditional chemical synthesis strategy. However, large amounts of toxic by-product, H2O2, should be eliminated through co-expressing catalase (Cat), thus severely increasing burden in cells. To efficiently and economically produce α-KG, here, the genes SpLGox (from Streptomyces platensis NTU3304) and SlCat (from Streptomyces lividans TK24) were inserted into the low-dosage-IPTG (Isopropyl β-D-Thiogalactoside) inducible expression system, constructed in our previous work, in E. coli, respectively. Besides, a double-strain catalysis system was established and optimized to produce α-KG, and the productivity of α-KG was increased 97% compared with that through single strain catalysis. Finally, a double-strain cultivation strategy was designed and employed to simplify the scale-up fermentation. Using the optimized whole-cell biocatalyst conditions (pH 7.0, 35 °C), majority of the L-glutamic acid was transformed into α-KG and the titer reached 95.4 g/L after 6 h with the highest productivity at present. Therefore, this strategy may efficiently and cost-effectively produce α-KG, enhancing its potential for industrial applications. KEY POINTS: • SpLGox and SlCat were over-expressed to catalyze L-Glu to α-KG and eliminate by-product H2O2, respectively. • Double-strain cultivation and catalysis system can efficiently and cost-effectively produce α-KG from L-Glu.

Metabolic engineering and fermentation optimization strategies for producing organic acids of the tricarboxylic acid cycle by microbial cell factories

The organic acids of the tricarboxylic acid (TCA) pathway are important platform compounds and are widely used in many areas. The high-productivity strains and high-efficient and low-cost fermentation are required to satisfy a huge market size. The high metabolic flux of the TCA pathway endows microorganisms potential to produce high titers of these organic acids. Coupled with metabolic engineering and fermentation optimization, the titer of the organic acids has been significantly improved in recent years. Herein, we discuss and compare the recent advances in synthetic pathway engineering, cofactor engineering, transporter engineering, and fermentation optimization strategies to maximize the biosynthesis of organic acids. Such engineering strategies were mainly based on the TCA pathway and glyoxylate pathway. Furthermore, organic-acid-secretion enhancement and renewable-substrate-based fermentation are often performed to assist the biosynthesis of organic acids. Further strategies are also discussed to construct high-productivity and acid-resistant strains for industrial large-scale production.

Multidimensional engineering of Escherichia coli for efficient biosynthesis of cis-3-hydroxypipecolic acid

Cis-3-hydroxypipecolic acid (cis-3-HyPip) is the crucial part of many alkaloids and drugs. However, its bio-based industrial production remains challenging. Here, lysine cyclodeaminase from Streptomyces malaysiensis (SmLCD) and pipecolic acid hydroxylase from Streptomyces sp. L-49973 (StGetF) were screened to achieve the conversion of L-lysine to cis-3-HyPip. Considering the high-cost of cofactors, NAD(P)H oxidase from Lactobacillus sanfranciscensis (LsNox) was further overexpressed in chassis strain Escherichia coli W3110 ΔsucCD (α-ketoglutarate-producing strain) to construct the NAD⁺ regeneration system, thus realizing the bioconversion of cis-3-HyPip from low-cost substrate L-lysine without NAD⁺ and α-ketoglutarate addition. To further accelerate the transmission efficiency of cis-3-HyPip biosynthetic pathway, multiple-enzyme expression optimization and transporter dynamic regulation via promoter engineering were conducted. Through fermentation optimization, the final engineered strain HP-13 generated 78.4 g/L cis-3-HyPip with 78.9% conversion in a 5-L fermenter, representing the highest production level achieved so far. These strategies described herein show promising potentials for large-scale production of cis-3-HyPip.

Metabolomic study on the quality differences and physiological characteristics between rice cultivated in drought and flood conditions

The differences between dry- and flood-cultivated rice and the reason behind low-quality dry-cultivated rice were clarified. The physiological traits, starch synthase activity, and grain metabolomics of 'Longdao 18' were measured and analyzed at four growth stages. The brown, milled, and whole-milled rice rates and AGPase, SSS, and SBE activity were lower after drought treatment than during flood cultivation, while the chalkiness, chalky grain rate, amylose (16.57-20.999%), protein (7.99-12.09%), and GBSS activity were higher. Related enzymatic gene expression showed significant differences. Metabolic results showed pyruvate, glycine, and methionine upregulation at 8DAF and higher citric, pyruvic, and α-ketoglutaric acid content at 15DAF. Therefore, 8DAF-15DAF represented the crucial quality formation period for dry-cultivated rice. At 8DAF, the respiratory pathways used amino acids as signaling molecules and alternative substrates to adapt to energy shortages, arid environments and rapid protein accumulation and synthesis. Excessive amylose synthesis at 15DAF accelerated reproductive growth, promoting rapid premature aging.

Application of cofactors in the regulation of microbial metabolism: A state of the art review

Cofactors are crucial chemicals that maintain cellular redox balance and drive the cell to do synthetic and catabolic reactions. They are involved in practically all enzymatic activities that occur in live cells. It has been a hot research topic in recent years to manage their concentrations and forms in microbial cells by using appropriate techniques to obtain more high-quality target products. In this review, we first summarize the physiological functions of common cofactors, and give a brief overview of common cofactors acetyl coenzyme A, NAD(P)H/NAD(P)+, and ATP/ADP; then we provide a detailed introduction of intracellular cofactor regeneration pathways, review the regulation of cofactor forms and concentrations by molecular biological means, and review the existing regulatory strategies of microbial cellular cofactors and their application progress, to maximize and rapidly direct the metabolic flux to target metabolites. Finally, we speculate on the future of cofactor engineering applications in cell factories. Graphical Abstract.

Metabolic engineering of Schizosaccharomyces pombe for itaconic acid production

The economical production of value-added chemicals from renewable biomass is a promising aspect of producing a sustainable economy. Itaconic acid (IA) is a high value-added compound that is expected to be an alternative to petroleum-based chemicals. In this study, we developed a metabolic engineering strategy for the large-scale production of IA from glucose using the fission yeast Schizosaccharomyces pombe. Heterologous expression of the cis-aconitic acid decarboxylase (CAD) gene from Aspergillus terreus, which encodes cis-aconitate decarboxylase in the cytosol, led to the production of 0.132 g/L of IA. We demonstrated that mitochondrial localization of CAD enhanced the production of IA. To prevent the leakage of carbon flux from the TCA cycle, we generated a strain in which the endogenous malate exporter, citrate lyase, and citrate transporter genes were disrupted. A titer of 1.110 g/L of IA was obtained from a culture of this strain started with 50 g/L of glucose. By culturing the multiple mutant strain at increased cell density, we succeeded in enhancing the IA production to 1.555 g/L. The metabolic engineering strategies presented in this study have the potential to improve the titer of the biosynthesis of derivatives of intermediates of the TCA cycle.

Application of a New Engineered Strain of Yarrowia lipolytica for Effective Production of Calcium Ketoglutarate Dietary Supplements

The present study aimed to develop a technology for the production of dietary supplements based on yeast biomass and α-ketoglutaric acid (KGA), produced by a new transformant of Yarrowia lipolytica with improved KGA biosynthesis ability, as well to verify the usefulness of the obtained products for food and feed purposes. Transformants of Y. lipolytica were constructed to overexpress genes encoding glycerol kinase, methylcitrate synthase and mitochondrial organic acid transporter. The strains were compared in terms of growth ability in glycerol- and oil-based media as well as their suitability for KGA biosynthesis in mixed glycerol-oil medium. The impact of different C:N:P ratios on KGA production by selected strain was also evaluated. Application of the strain that overexpressed all three genes in the culture with a C:N:P ratio of 87:5:1 allowed us to obtain 53.1 g/L of KGA with productivity of 0.35 g/Lh and yield of 0.53 g/g. Finally, the possibility of obtaining three different products with desired nutritional and health-beneficial characteristics was demonstrated: (1) calcium α-ketoglutarate (CaKGA) with purity of 89.9% obtained by precipitation of KGA with CaCO3, (2) yeast biomass with very good nutritional properties, (3) fixed biomass-CaKGA preparation containing 87.2 μg/g of kynurenic acid, which increases the health-promoting value of the product.

Neothalfine, a potent natural anti-tumor agent against metastatic colorectal cancer and its primary mechanism

Neothalfine is a natural bisbenzylisoquinoline alkaloid with the abundant resource in medicinal plants and has not been reported its anti-tumor efficacy. In the present study, the anti-tumor efficacy was investigated and it showed broad-spectrum activity against several cancer cell lines, especially metastatic colorectal cancer (HCT116, SW620, T84) with the IC50 values of 7.2, 5.9, 8.2 nM, respectively, roughly equal to well-known anti-tumor agent docetaxel (4.0, 4.7, 2.7 nM) and nearly 1000 folds than CPT-11 (4.4, 5.1, 6.9 μM). Furthermore, neothalfine inhibited colorectal cell proliferation by resulting in cell cycle arrest at the G2/M phase and induced apoptosis through the dysfunction of mitochondria to trigger intrinsic apoptotic pathway by untargeted metabolomic method, mitochondrial membrane potential, and caspase-3/7 activity assay. Moreover, neothalfine damaged colorectal cancer clonal spheres expansion significantly at the concentration of 3.5 nM with nearly 1000 folds efficacy than CPT-11 (3.0 µM). The results supported that neothalfine might be an anti-tumor lead for further investigation.

Fitness of Chassis Cells and Metabolic Pathways for l-Cysteine Overproduction in Escherichia coli

l-Cysteine is a ubiquitous and unique sulfur-containing amino acid with numerous applications in agricultural and food industries. The efficient production of l-cysteine via microbial fermentation has received a great deal of attention. In this study, the fitness of different Escherichia coli K-12 strains harboring plasmid pLH03 was investigated. The enhancement of the precursor synthetic pathway and thiosulfate assimilation pathway resulted in the good performance of the E. coli BW25113 strain. The expression levels of synthetic pathway genes were optimized by two constitutive promoters to assess their effects on cysteine production. In conjunction, the main degradation pathway genes were also deleted for more efficient production of cysteine. l-Cysteine production was further increased through the manipulation of the sulfur transcription regulator cysB and sulfur supplementation. After process optimization in a 1.5 L bioreactor, LH2A1M0BΔYTS-pLH03 [BW25113 Ptrc2-serA Ptrc1-cysMPtrc-cysBΔyhaMΔtnaAΔsdaA-(pLH03)] accumulated 8.34 g/L cysteine, laying a foundation for application in the cysteine fermentation industry.

Pathway engineering of Escherichia coli for one-step fermentative production of L-theanine from sugars and ethylamine

L-theanine is the most abundant free amino acid in tea that offers various favorable physiological and pharmacological effects. Bacterial enzyme of γ-glutamylmethylamide synthetase (GMAS) can catalyze the synthesis of theanine from glutamate, ethylamine and ATP, but the manufacturing cost is uncompetitive due to the expensive substrates and complex processes. In this study, we described pathway engineering of wild-type Escherichia coli for one-step fermentative production of theanine from sugars and ethylamine. First, the synthetic pathway of theanine was conducted by heterologous introduction of a novel GMAS from Paracoccus aminovorans. A xylose-induced T7 RNA polymerase-P_T7 promoter system was used to enhance and control gmas gene expression. Next, the precursor glutamate pool was increased by overexpression of native citrate synthase and introduction of glutamate dehydrogenase from Corynebacterium glutamicum. Then, in order to push more carbon flux towards theanine synthesis, the tricarboxylic acid cycle was interrupted and pyruvate carboxylase from C. glutamicum was introduced as a bypath supplying oxaloacetate from pyruvate. Finally, an energy-conserving phosphoenolpyruvate carboxykinase from Mannheimia succiniciproducens was introduced to increase ATP yield for theanine synthesis. After optimizing the addition time and concentration of ethylamine hydrochloride in the fed-batch fermentation, the recombinant strain TH11 produced 70.6 ​g/L theanine in a 5-L bioreactor with a yield and productivity of 0.42 ​g/g glucose and 2.72 ​g/L/h, respectively. To our knowledge, this is the first report regarding the pathway engineering of E. coli for fermentative production of theanine. The high production capacity of recombinant strain, combined with the easy processes, will hold attractive industrial application potential for the future.

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γ-Glutamylmethylamide synthetase from P. aminovorans showed high ligation activity.

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Xylose-induced T7 RNA polymerase-P_T7 promoter system was used to control gene expression.

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TCA cycle was rewired to push more carbon flux toward theanine synthesis.

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Ethylamine feeding strategy was optimized to balance cell growth and theanine production.

Engineering the transmission efficiency of the noncyclic glyoxylate pathway for fumarate production in Escherichia coli

BACKGROUND

Fumarate is a multifunctional dicarboxylic acid in the tricarboxylic acid cycle, but microbial engineering for fumarate production is limited by the transmission efficiency of its biosynthetic pathway.

RESULTS

Here, pathway engineering was used to construct the noncyclic glyoxylate pathway for fumarate production. To improve the transmission efficiency of intermediate metabolites, pathway optimization was conducted by fluctuating gene expression levels to identify potential bottlenecks and then remove them, resulting in a large increase in fumarate production from 8.7 to 16.2 g/L. To further enhance its transmission efficiency of targeted metabolites, transporter engineering was used by screening the C₄-dicarboxylate transporters and then strengthening the capacity of fumarate export, leading to fumarate production up to 18.9 g/L. Finally, the engineered strain E. coli W3110△4-P_(H)CAI_(H)SC produced 22.4 g/L fumarate in a 5-L fed-batch bioreactor.

CONCLUSIONS

In this study, we offered rational metabolic engineering and flux optimization strategies for efficient production of fumarate. These strategies have great potential in developing efficient microbial cell factories for production of high-value added chemicals.