Modular metabolic engineering for production of phloretic acid, phloretin and phlorizin in Escherichia coli

De Novo Artificial Biosynthesis of 3-Hydroxyphloretin in Escherichia coli

3-Hydroxyphloretin (3-OH phloretin), a dihydrochalcone compound containing a catechol moiety, is naturally present in apples and exhibits potent anti-adipogenic, anti-obesity, and anticancer activities. In this study, we developed a modular co-culture platform enabling the de novo biosynthesis of 3-OH phloretin from glucose in Escherichia coli. We demonstrated that 4-coumarate 3-hydroxylase (Sam5), derived from Saccharothrix espanaensis, efficiently catalyzes the hydroxylation of phloretin to 3-OH phloretin. The engineered co-culture system comprised two functional modules: an upstream module that converts l-tyrosine to phloretic acid through the expression of tyrosine ammonia-lyase and enoate reductase genes, and a downstream module that converts phloretic acid to 3-OH phloretin via the sequential action of 4-coumarate-CoA ligase, a mutated chalcone synthase, and Sam5. Using this system, we successfully achieved the de novo production of 3-OH phloretin at a titer of 4.69 mg/L from glucose. In parallel, the artificial biosynthetic pathway also yielded phloretic acid and 3-hydroxyphloretic acid (3-OH phloretic acid) at titers of 161.7 and 176.2 mg/L, respectively, in an engineered l-tyrosine-overproducing E. coli strain. To the best of our knowledge, this study represents the first successful establishment of an artificial biosynthetic route for the production of both 3-OH phloretic acid and 3-OH phloretin directly from glucose in E. coli. This platform lays the groundwork for the microbial production of valuable dihydrochalcone compounds and holds promise for further optimization toward industrial-scale applications.

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.

Via Air or Rhizosphere: The Phytotoxicity of Nepeta Essential Oils and Malus Dihydrochalcones

Many specialized metabolites found in plants have significant potential for developing environmentally friendly weed management solutions. This review focuses on the phytotoxic effects of volatile terpenes and phenolic compounds, particularly nepetalactone, an iridoid monoterpenoid from Nepeta species, and phloretin, a dihydrochalcone predominantly found in the genus Malus. We highlight current findings on their herbicidal effects, including morphological, physiological, and biochemical responses in target plants. These results underscore their potential for developing sustainable herbicides that could control weeds with minimal environmental impact. We also discuss their soil persistence and methods to enhance their solubility, chemical stability, and bioavailability. Additionally, the possible effects on non-target organisms, such as pollinators, non-pollinating insects, and soil microbiota, are considered. However, further research and a deeper understanding of their long-term ecological impact, along with a resistance development risk assessment, is essential for the potential development of bioherbicides that could be applied in sustainable weed management practices.

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.

Biochemical characterization of HcrF from Limosilactobacillus fermentum, a NADH-dependent 2-ene reductase with activity on hydroxycinnamic acids

In fermented plant foods, phenolic compounds are metabolized by 2-ene reductases, which reduce double bonds adjacent to an aromatic rings in phytochemicals, including hydroxycinnamic acids, isoflavones, and flavones. Only few 2-ene reductases of lactic acid bacteria were characterized, including the hydrocinnamic reductases HcrB and Par1, and the daidzein reductase of Lactococcus lactis. This study aimed to characterize HcrF, a homologue of HcrB, in Limosilactobacillus fermentum. HcrF was purified after cloning in Escherichia coli and purification by affinity chromatography. HcrF was optimally active at 30°C-40°C and pH 7.0 and required both flavin mononucleotide and nicotinamide adenine dinucleotide as co-factors. Ferulic, caffeic, p-coumaric, and sinapic acids but not trans-cinnamic acids were reduced to dihydro derivatives. The maximum reaction velocity Vmax of HcrF was highest for ferulic acid. On a phylogenetic tree of 2-ene reductases, HcrF clustered most closely with the hydroxycinnamic acid reductase HcrB of Lactiplantibacillus plantarum. The hydroxycinnamic acid reductase Par1 of Furfurilactobacillus milii and flavone or isoflavone reductases were only distantly related to HcrF. In summary, current knowledge does not allow to predict the substrate specificity of 2-ene reductases on the basis of the protein sequence; this study adds HcrF to the short list of enzymes with known substrate specificity.

Self-controlled in silico gene knockdown strategies to enhance the sustainable production of heterologous terpenoid by Saccharomyces cerevisiae

Microbial bioengineering is a growing field for producing plant natural products (PNPs) in recent decades, using heterologous metabolic pathways in host cells. Once heterologous metabolic pathways have been introduced into host cells, traditional metabolic engineering techniques are employed to enhance the productivity and yield of PNP biosynthetic routes, as well as to manage competing pathways. The advent of computational biology has marked the beginning of a novel epoch in strain design through in silico methods. These methods utilize genome-scale metabolic models (GEMs) and flux optimization algorithms to facilitate rational design across the entire cellular metabolic network. However, the implementation of in silico strategies can often result in an uneven distribution of metabolic fluxes due to the rigid knocking out of endogenous genes, which can impede cell growth and ultimately impact the accumulation of target products. In this study, we creatively utilized synthetic biology to refine in silico strain design for efficient PNPs production. OptKnock simulation was performed on the GEM of Saccharomyces cerevisiae OA07, an engineered strain for oleanolic acid (OA) bioproduction that has been reported previously. The simulation predicted that the single deletion of fol1, fol2, fol3, abz1, and abz2, or a combined knockout of hfd1, ald2 and ald3 could improve its OA production. Consequently, strains EK1∼EK7 were constructed and cultivated. EK3 (OA07△fol3), EK5 (OA07△abz1), and EK6 (OA07△abz2) had significantly higher OA titers in a batch cultivation compared to the original strain OA07. However, these increases were less pronounced in the fed-batch mode, indicating that gene deletion did not support sustainable OA production. To address this, we designed a negative feedback circuit regulated by malonyl-CoA, a growth-associated intermediate whose synthesis served as a bypass to OA synthesis, at fol3, abz1, abz2, and at acetyl-CoA carboxylase-encoding gene acc1, to dynamically and autonomously regulate the expression of these genes in OA07. The constructed strains R_3A, R_5A and R_6A had significantly higher OA titers than the initial strain and the responding gene-knockout mutants in either batch or fed-batch culture modes. Among them, strain R_3A stand out with the highest OA titer reported to date. Its OA titer doubled that of the initial strain in the flask-level fed-batch cultivation, and achieved at 1.23 ± 0.04 g L-1 in 96 h in the fermenter-level fed-batch mode. This indicated that the integration of optimization algorithm and synthetic biology approaches was efficiently rational for PNP-producing strain design.

Phloretin: a comprehensive review of its potential against diabetes and associated complications

OBJECTIVES

Phloretin is ubiquitous in apples (Malus domestica) and other fruits and has potential antidiabetic properties. Considering the preclinical potential of phloretin, its transition to clinical observations has unintentionally been neglected, particularly within the diabetic population. Furthermore, a comprehensive understanding of its pharmacokinetics remains elusive. This review seeks to offer valuable insights into phloretin's physical properties, pharmacokinetics, and pharmacodynamics, aiming to unveil opportunities for additional research on its therapeutic potential in the context of diabetes.

KEY FINDINGS

All pharmacokinetic reports of phloretin confirm that the utilization of phloretin gets enhanced during diabetic conditions. Phloretin targets pathomechanisms such as glucose transporter 4 (GLUT4) and peroxisome proliferator's activity-activated receptor-γ (PPAR-γ) to decrease insulin resistance in diabetic conditions. Moreover, phloretin targets inflammatory, oxidative, and apoptotic signaling to minimize the progression of diabetes-associated macro- and microvascular complications.

SUMMARY

The pleiotropic antidiabetic action of phloretin is mainly dependent on its pharmacokinetics. Nevertheless, further investigation into the altered pharmacokinetics of phloretin during diabetic conditions is essential. Additionally, the results derived from clinical studies utilized apples, apple extract, and supplements containing phloretin. Greater emphasis should be placed on future clinical studies to assess the potential of phloretin as a standalone compound.

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.

Modular Engineering of Saccharomyces cerevisiae for De Novo Biosynthesis of Genistein

Genistein, a nutraceutical isoflavone, has various pharmaceutical and biological activities which benefit human health via soy-containing food intake. This study aimed to construct Saccharomyces cerevisiae to produce genistein from sugar via a modular engineering strategy. In the midstream module, various sources of chalcone synthases and chalcone isomerase-like proteins were tested which enhanced the naringenin production from p-coumaric acid by decreasing the formation of the byproduct. The upstream module was reshaped to enhance the metabolic flux to p-coumaric acid from glucose by overexpressing the genes in the tyrosine biosynthetic pathway and deleting the competing genes. The downstream module was rebuilt to produce genistein from naringenin by pairing various isoflavone synthases and cytochrome P450 reductases. The optimal pair was used for the de novo biosynthesis of genistein with a titer of 31.02 mg/L from sucrose at 25 °C. This is the first report on the de novo biosynthesis of genistein in engineered S. cerevisiae to date. This work shows promising potential for producing flavonoids and isoflavonoids by modular metabolic engineering.

Synthetic spatial patterning in bacteria: advances based on novel diffusible signals

Engineering multicellular patterning may help in the understanding of some fundamental laws of pattern formation and thus may contribute to the field of developmental biology. Furthermore, advanced spatial control over gene expression may revolutionize fields such as medicine, through organoid or tissue engineering. To date, foundational advances in spatial synthetic biology have often been made in prokaryotes, using artificial gene circuits. In this review, engineered patterns are classified into four levels of increasing complexity, ranging from spatial systems with no diffusible signals to systems with complex multi-diffusor interactions. This classification highlights how the field was held back by a lack of diffusible components. Consequently, we provide a summary of both previously characterized and some new potential candidate small-molecule signals that can regulate gene expression in Escherichia coli. These diffusive signals will help synthetic biologists to successfully engineer increasingly intricate, robust and tuneable spatial structures.

Systems Metabolic Engineering of Escherichia coli Coculture for De Novo Production of Genistein

Genistein is a plant-derived isoflavone possessing various bioactivities to prevent aging, carcinogenesis, and neurodegenerative and inflammation diseases. As a typical complex flavonoid, its microbial production from sugar remains to be completed. Here, we use systems metabolic engineering stategies to design and develop a three-strain commensalistic Escherichia coli coculture that for the first time realized the de novo production of genistein. First, we reconstituted the naringenin module by screening and incorporating chalcone isomerase-like protein, an auxiliary component to rectify the chalcone synthase promiscuity. Furthermore, we devised and constructed the genistein module by N-terminal modifications of plant P450 enzyme 2-hydroxyisoflavanone synthase and cytochrome P450 enzyme reductase. When naringenin-producing strain was cocultivated with p-coumaric acid-overproducing strain (a phenylalanine-auxotroph), two-strain coculture worked as commensalism through a unidirectional nutrient flow, which favored the efficient production of naringenin with a titer of 206.5 mg/L from glucose. A three-strain commensalistic coculture was subsequently engineered, which produced the highest titer to date of 60.8 mg/L genistein from a glucose and glycerol mixture. The commensalistic coculture is a flexible and versatile platform for the production of flavonoids, indicating a promising future for production of complex natural products in engineered E. coli.

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

Kaempferide, a plant-derived natural flavonoid, exhibits excellent pharmacological activities with nutraceutical and medicinal applications in human healthcare. Efficient microbial production of complex flavonoids suffers from metabolic crosstalk and burden, which is a big challenge for synthetic biology. Herein, we identified 4'-O-methyltransferases and divided the artificial biosynthetic pathway of kaempferide into upstream, midstream, and downstream modules. By combining heterologous genes from different sources and fine-tuning the expression, we optimized each module for the production of kaempferide. Furthermore, we designed and evaluated four division patterns of synthetic labor in coculture systems by plug-and-play modularity. The linear division of three modules in a three-strain coculture showed higher productivity of kaempferide than that in two-strain cocultures. The U-shaped division by co-distributing the upstream and downstream modules in one strain led to the best performance of the coculture system, which produced 116.0 ± 3.9 mg/L kaempferide, which was 510, 140, and 50% higher than that produced by the monoculture, two-strain coculture, and three-strain coculture with the linear division, respectively. This is the first report of efficient de novo production of kaempferide in a robust Escherichia coli coculture. The strategy of U-shaped pathway division in the coculture provides a promising way for improving the productivity of valuable and complex natural products.