Metabolic Division in an Escherichia coli Coculture System for Efficient Production of Kaempferide

Efficient biosynthesis of gallic acid by a syntrophic Escherichia coli co-culture system

Gallic acid (GA), a natural phenolic acid antioxidant, has significant therapeutic and industrial applications. However, its traditional manufacturing approach, based on plant extraction, has been associated with risks of environmental pollution as well as a limited range of applications. Consequently, microbial-based production of GA, being more environmental-friendly, is viewed as a potential alternative. This study reports the efficient biosynthesis of GA from renewable glucose via a syntrophic Escherichia coli co-culture system. An effective GA biosynthesis pathway was first analyzed and determined. Then the rate-limiting step involving the hydroxylation of protocatechuic acid (PCA) to GA was removed by integrating multiple copies of the key gene pobAT294A/Y385F into the chromosome of a PCA-overproducing strain. The resulting strain GA10 produced 41.88 g/L GA with a yield of 0.185 mol/mol, but up to 9.54 g/L of the intermediate PCA accumulated in the fermentation broth. To overcome this issue, a catalytic strain COT03 was constructed by coupling the metabolism of excess intracellular NADPH supply with the NADPH-consuming reaction catalyzed by PobAT294A/Y385F. This yielded a syntrophic E. coli co-culture system that consisted of a GA-overproducing strain (GA10) and a growth-coupled biocatalytic strain (COT03). Following optimization of the culture conditions, the co-culture system produced 57.66 g/L GA from glucose within 75 h, with a yield of 0.233 mol/mol and an average productivity of 0.769 g/L/h. This study lays the foundation for the potential industrial biomanufacturing of GA from glucose.

Recent advances in microbial synthesis of polyphenols

Polyphenols are plant-derived secondary metabolites known for their antioxidants, anti-inflammatory, and antimicrobial properties, with flavonoids being the most structurally diverse and medically relevant subclass. Traditional plant extraction is limited by low abundance and difficulty in separating from analogs. Microbial synthesis has emerged as an alternative method to complement plant extraction. This review summarizes recent advancements in microbe-sourced polyphenols, especially flavonoids and related derivatives. Key strategies, including modular design, CRISPR-based optimization, co-culture, and dynamic regulatory systems, have been employed to enhance microbial factory production efficiency. Emerging artificial intelligence-driven computational modeling and pathway optimization hold significant promise for enhancing polyphenol biosynthesis. Taken together, microbial synthesis offers a scalable and sustainable alternative to plant extraction. The cost-effective production of polyphenols will expand their applications in pharmaceuticals, nutraceuticals, and food industry.

Metabolic division engineering of Escherichia coli consortia for de novo biosynthesis of flavonoids and flavonoid glycosides

Heterologous biosynthesis of natural products with long biosynthetic pathways in microorganisms often suffers from diverse problems, such as enzyme promiscuity and metabolic burden. Flavonoids and their glycosides are important phytochemicals in the diet of human beings, with various health benefits and biological activities. Despite previous efforts and achievements, efficient microbial production of plant-derived flavonoid compounds with long pathways remains challenging. Herein, we applied metabolic division engineering of Escherichia coli consortia to overcome these limitations. By establishing new biosynthetic pathways, rationally adjusting metabolic node intermediates, and engineering different auxotrophic and orthogonal carbon sources for hosts, we established stable two- and three-bacteria co-culture systems to efficiently de novo produce 12 flavonoids (61.15-325.31 mg/L) and 36 corresponding flavonoid glycosides (1.31-191.79 mg/L). Furthermore, the co-culture system was rapidly extended in a plug-and-play manner to produce isoflavonoids, dihydrochalcones, and their glycosides. This study successfully alleviates metabolic burden and overcomes enzyme promiscuity, and provides significant insights that could guide the biosynthesis of other complex secondary metabolites.

De novo biosynthesis of quercetin in Yarrowia Lipolytica through systematic metabolic engineering for enhanced yield

Kaempferol and quercetin possess various biological activities, making them valuable in food and medicine. However, their production via traditional methods is often inefficient. This study aims to address this gap by engineering the yeast Yarrowia lipolytica to achieve high yields of these flavonoids. We designed a kaempferol biosynthetic pathway by integrating multiple-copy fusion enzyme expression modules, F3H-(GGGGS)2-FLS, into the genome with an optimized linker (GGGGS)2 to enhance kaempferol production from naringenin. To synthesize quercetin de novo, we introduced the FMOCPR gene into the kaempferol-synthesizing strain using the optimized pFBAin promoter. Notably, increasing glucose concentration effectively boosted the production of both flavonoids. Our results demonstrated kaempferol and quercetin titers reaching 194.30 ± 7.69 and 278.92 ± 11.58 mg/L, respectively, in shake-flask cultures. These findings suggest that Y. lipolytica is a promising platform for the efficient production of flavonoid-derived products.

Construction and Optimization of Engineered Saccharomyces cerevisiae for De Novo Synthesis of Phloretin and Its Derivatives

Phloretin and its derivatives are dihydrochalcone compounds with diverse pharmacological properties and biological activities, offering significant potential for applications in the food and pharmaceutical industries. Due to their structural similarity to flavonoids, their extraction and isolation were highly challenging. Although the biosynthesis of phloretin via three distinct pathways has been reported, a systematic comparison within the same host has yet to be conducted. In this study, we employed rational design and synthetic biology approaches to engineer Saccharomyces cerevisiae for de novo synthesis of phloretin and its derivatives. We constructed and evaluated three biosynthetic pathways for phloretin in S. cerevisiae, demonstrating that effective phloretin synthesis is achievable only via the p-coumaryl-CoA pathway. Additionally, by optimizing enzyme screening, strain engineering, and coordinating heterologous pathways with endogenous metabolism, we achieved the highest reported de novo titer of 287.2 mg/L for phloretin, 184.6 mg/L for phlorizin, 103.1 mg/L for trilobatin, and 164.5 mg/L for nothofagin and the first-time synthesis of 4-methylphloretin and hesperetin dihydrochalcone. This study was committed to addressing the growing demand for dihydrochalcones while laying the foundation for the biosynthesis of more complex derivatives.

Strategies and tools to construct stable and efficient artificial coculture systems as biosynthetic platforms for biomass conversion

Inspired by the natural symbiotic relationships between diverse microbial members, researchers recently focused on modifying microbial chassis to create artificial coculture systems using synthetic biology tools. An increasing number of scientists are now exploring these systems as innovative biosynthetic platforms for biomass conversion. While significant advancements have been achieved, challenges remain in maintaining the stability and productivity of these systems. Sustaining an optimal population ratio over a long time period and balancing anabolism and catabolism during cultivation have proven difficult. Key issues, such as competitive or antagonistic relationships between microbial members, as well as metabolic imbalances and maladaptation, are critical factors affecting the stability and productivity of artificial coculture systems. In this article, we critically review current strategies and methods for improving the stability and productivity of these systems, with a focus on recent progress in biomass conversion. We also provide insights into future research directions, laying the groundwork for further development of artificial coculture biosynthetic platforms.

Mid-Long Chain Dicarboxylic Acid Production via Systems Metabolic Engineering: Progress and Prospects

Mid-to-long-chain dicarboxylic acids (DCAi, i ≥ 6) are organic compounds in which two carboxylic acid functional groups are present at the terminal position of the carbon chain. These acids find important applications as structural components and intermediates across various industrial sectors, including organic compound synthesis, food production, pharmaceutical development, and agricultural manufacturing. However, conventional petroleum-based DCA production methods cause environmental pollution, making sustainable development challenging. Hence, the demand for eco-friendly processes and renewable raw materials for DCA production is rising. Owing to advances in systems metabolic engineering, new tools from systems biology, synthetic biology, and evolutionary engineering can now be used for the sustainable production of energy-dense biofuels. Here, we explore systems metabolic engineering strategies for DCA synthesis in various chassis via the conversion of different raw materials into mid-to-long-chain DCAs. Subsequently, we discuss the future challenges in this field and propose synthetic biology approaches for the efficient production and successful commercialization of these acids.

Efficient production of γ-aminobutyric acid using engineered Escherichia coli whole-cell catalyst

γ-Aminobutyric acid (GABA) has been widely used in the food, feed, pharmaceutical, and chemical industry fields. Previously, we developed a whole-cell catalyst capable of converting L-glutamate (L-Glu) into GABA by overexpressing the glutamate decarboxylase gene (gadz11) from Bacillus sp. Z11 in Escherichia coli BL21(DE3). However, to enhance cell permeability, a freeze-thaw treatment is required, and to enhance GADZ11 activity, pyridoxal 5'-phosphate (PLP) must be added to the reaction system. The aim of this study is to provide a more efficient approach for GABA production by engineering the recombinant E. coli above. First, the inducible expression conditions of the gadz11 in E. coli were optimized to 37 °C for 6 h. Next, an ideal engineered strain was produced via increasing cell permeability by overexpressing sulA and eliminating PLP dependence by constructing a self-sufficient system. Furthermore, an efficient whole-cell biocatalytic process was optimized. The optimal substrate concentration, cell density, and reaction temperature were 1.0 mol/L (the molecular ratio of L-Glu to L-monosodium glutamate (L-MSG) was 4:1), 15 and 37 °C, respectively. Finally, a whole-cell bioconversion procedure was performed in a 3-L bioreactor under optimal conditions. The strain could be reused for at least two cycles with GABA yield, productivity and conversion ratio of 206.2 g/L, 117.8 g/L/h and 100.0%, respectively. This is currently the highest GABA productivity from a mixture of L-Glu and L-MSG reported without the addition of cofactors or additional treatment of cells. This work demonstrates that the novel engineered E. coli strain has the potential for application in large-scale industrial GABA production.

Mitigative potential of kaempferide against polyethylene microplastics induced testicular damage by activating Nrf-2/Keap-1 pathway

Polyethylene microplastics (PE-MPs) are one of the environmental contaminants that instigate oxidative stress (OS) in various organs of the body, including testes. Kaempferide (KFD) is a plant-derived natural flavonol with potential neuroprotective, hepatoprotective, anti-cancer, anti-oxidant and anti-inflammatory properties. Therefore, the present study was designed to evaluate the alleviative effects of KFD against PE-MPs-prompted testicular toxicity in rats. Fourty eight adult male albino rats were randomly distributed into 4 groups: control, PE-MPs-administered (1.5 mgkg-1), PE-MPs (1.5 mgkg-1) + KFD (20 mgkg-1) co-treated and KFD (20 mgkg-1) only treated group. PE-MPs intoxication significantly (P < 0.05) lowered the expression of Nrf-2 and anti-oxidant enzymes, while increasing the expression of Keap-1. The activities of anti-oxidants i.e., catalase (CAT), glutathione reductase (GSR), superoxide dismutase (SOD), hemeoxygene-1 (HO-1) and glutathione peroxidase (GPx) were reduced, besides malondialdehyde (MDA) and reactive oxygen species (ROS) contents were increased significantly (P < 0.05) following the PE-MPs exposure. Moreover, PE-MPs exposure significantly (P < 0.05) reduced the sperm motility, viability and count, whereas considerably (P < 0.05) increased the dead sperm number and sperm structural anomalies. Furthermore, PE-MPs remarkably (P < 0.05) decreased steroidogenic enzymes and Bcl-2 expression, while increasing the expression of Caspase-3 and Bax. PE-MPs exposure significantly (P < 0.05) reduced the levels of follicle-stimulating hormone (FSH), luteinizing hormone (LH) and testosterone, whereas inflammatory indices were increased. PE-MPs exposure also induced significant histopathological damages in the testes. Nevertheless, KFD supplementation significantly (P < 0.05) abrogated all the damages induced by PE-MPs. The findings of our study demonstrated that KFD could significantly attenuate PE-MPs-instigated OS and testicular toxicity, due to its anti-oxidant, anti-inflammatory, androgenic and anti-apoptotic potential.

Challenges and opportunities for engineered Escherichia coli as a pivotal chassis toward versatile tyrosine-derived chemicals production

Growing concerns over limited fossil resources and associated environmental problems are motivating the development of sustainable processes for the production of high-volume fuels and high-value-added compounds. The shikimate pathway, an imperative pathway in most microorganisms, is branched with tyrosine as the rate-limiting step precursor of valuable aromatic substances. Such occurrence suggests the shikimate pathway as a promising route in developing microbial cell factories with multiple applications in the nutraceutical, pharmaceutical, and chemical industries. Therefore, an increasing number of studies have focused on this pathway to enable the biotechnological manufacture of pivotal and versatile aromatic products. With advances in genome databases and synthetic biology tools, genetically programmed Escherichia coli strains are gaining immense interest in the sustainable synthesis of chemicals. Engineered E. coli is expected to be the next bio-successor of fossil fuels and plants in commercial aromatics synthesis. This review summarizes successful and applicable genetic and metabolic engineering strategies to generate new chassis and engineer the iterative pathway of the tyrosine route in E. coli, thus addressing the opportunities and current challenges toward the realization of sustainable tyrosine-derived aromatics.

Construction of Coculture System Containing Escherichia coli with Different Microbial Species for Biochemical Production

Microbial synthesis of target chemicals usually involves multienzymatic reactions in vivo, especially for compounds with a long metabolic pathway. However, when various genes are introduced into one single strain, it leads to a heavy metabolic burden. In contrast, the microbial coculture system can allocate metabolic pathways into different hosts, which will relieve the metabolic burdens. Escherichia coli is the most used chassis to synthesize biofuels and chemicals owing to its well-known genetics, high transformation efficiency, and easy cultivation. Accordingly, cocultures containing the cooperative E. coli with other microbial species have received great attention. In this review, the individual applications and boundedness of different combinations will be summarized. Additionally, the strategies for the self-regulation of population composition, which can help enhance the stability of a coculture system, will also be discussed. Finally, perspectives for the cocultures will be proposed.

Modular Metabolic Engineering and Synthetic Coculture Strategies for the Production of Aromatic Compounds in Yeast

Microbial-derived aromatics provide a sustainable and renewable alternative to petroleum-derived chemicals. In this study, we used the model yeast Saccharomyces cerevisiae to produce aromatic molecules by exploiting the concept of modularity in synthetic biology. Three different modular approaches were investigated for the production of the valuable fragrance raspberry ketone (RK), found in raspberry fruits and mostly produced from petrochemicals. The first strategy used was modular cloning, which enabled the generation of combinatorial libraries of promoters to optimize the expression level of the genes involved in the synthesis pathway of RK. The second strategy was modular pathway engineering and involved the creation of four modules, one for product formation: RK synthesis module (Mod. RK); and three for precursor synthesis: aromatic amino acid synthesis module (Mod. Aro), p-coumaric acid synthesis module (Mod. p-CA), and malonyl-CoA synthesis module (Mod. M-CoA). The production of RK by combinations of the expression of these modules was studied, and the best engineered strain produced 63.5 mg/L RK from glucose, which is the highest production described in yeast, and 2.1 mg RK/g glucose, which is the highest yield reported in any organism without p-coumaric acid supplementation. The third strategy was the use of modular cocultures to explore the effects of division of labor on RK production. Two two-member communities and one three-member community were created, and their production capacity was highly dependent on the structure of the synthetic community, the inoculation ratio, and the culture media. In certain conditions, the cocultures outperformed their monoculture controls for RK production, although this was not the norm. Interestingly, the cocultures showed up to 7.5-fold increase and 308.4 mg/L of 4-hydroxy benzalacetone, the direct precursor of RK, which can be used for the semi-synthesis of RK. This study illustrates the utility of modularity in synthetic biology tools and their applications to the synthesis of products of industrial interest.

Biological valorization of lignin to flavonoids

Lignin is the most affluent natural aromatic biopolymer on the earth, which is the promising renewable source for valuable products to promote the sustainability of biorefinery. Flavonoids are a class of plant polyphenolic secondary metabolites containing the benzene ring structure with various biological activities, which are largely applied in health food, pharmaceutical, and medical fields. Due to the aromatic similarity, microbial conversion of lignin derived aromatics to flavonoids could facilitate flavonoid biosynthesis and promote the lignin valorization. This review thereby prospects a novel valorization route of lignin to high-value natural products and demonstrates the potential advantages of microbial bioconversion of lignin to flavonoids. The biodegradation of lignin polymers is summarized to identify aromatic monomers as momentous precursors for flavonoid synthesis. The biosynthesis pathways of flavonoids in both plants and strains are introduced and compared. After that, the key branch points and important intermediates are clearly discussed in the biosynthesis pathways of flavonoids. Moreover, the most significant enzyme reactions including Claisen condensation, cyclization and hydroxylation are demonstrated in the biosynthesis pathways of flavonoids. Finally, current challenges and potential future strategies are also discussed for transforming lignin into various flavonoids. The holistic microbial conversion routes of lignin to flavonoids could make a sustainable production of flavonoids and improve the feasibility of lignin valorization.

Microbial production of valuable chemicals by modular co-culture strategy

Nowadays, microbial synthesis has become a common way for producing valuable chemicals. Traditionally, microbial production of valuable chemicals is accomplished by a single strain. For the purpose of increasing the production titer and yield of a recombinant strain, complicated pathways and regulation layers should be fine-tuned, which also brings a heavy metabolic burden to the host. In addition, utilization of various complex and mixed substrates further interferes with the normal growth of the host strain and increases the complexity of strain engineering. As a result, modular co-culture technology, which aims to divide a target complex pathway into separate modules located at different single strains, poses an alternative solution for microbial production. Recently, modular co-culture strategy has been employed for the synthesis of different natural products. Therefore, in this review, various chemicals produced with application of co-cultivation technology are summarized, including co-culture with same species or different species, and regulation of population composition between the co-culture members. In addition, development prospects and challenges of this promising field are also addressed, and possible solution for these issues were also provided.