Recent advancement of engineering microbial hosts for the biotechnological production of flavonoids

Integrated metabolome and transcriptome analysis reveals the regulatory mechanism of low nitrogen-driven biosynthesis of saponins and flavonoids in Panax notoginseng

BACKGROUND

Nitrogen (N) is an important macronutrient involved in the biosynthesis of primary and secondary metabolites in plants. However, the metabolic regulatory mechanism of low-N-induced triterpenoid saponin and flavonoid accumulation in rhizomatous medicinal Panax notoginseng (Burk.) F. H. Chen remains unclear.

METHODS

To explore the potential regulatory mechanism and metabolic basis controlling the response of P. notoginseng to N deficiency, the transcriptome and metabolome were analysed in the roots.

RESULTS

The N content was significantly reduced in roots of N0-treated P. notoginseng (0 kg·N·667 m-2). The C/N ratio was enhanced in the N-deficient P. notoginseng. N deficiency promotes the accumulation of amino acids (L-proline, L-leucine, L-isoleucine, L-norleucine, L-arginine, and L-citrulline) and sugar (arabinose, xylose, glucose, fructose, and mannose), thus providing precursor metabolites for the biosynthesis of flavonoids and triterpenoid saponins. Downregulation of key structural genes (PAL, PAL3, ACC1, CHS2, PPO, CHI3, F3H, DFR, and FGT), in particular with the key genes of F3H, involved in the flavonoid biosynthesis pathway possibly induced the decrease in flavonoid content with increased N supply. Notoginsenoside R1, ginsenoside Re, Rg1, Rd, F1, R1 + Rg1 + Rb1 and total triterpenoid saponins were enhanced in the N0 groups than in the N15 (15 kg·N·667 m-2) plants. Higher phosphoenolpyruvate (an intermediate of glycolyticwith pathway metabolism) and serine (an intermediate of photorespiration) levels induced by N deficiency possibly promote saponin biosynthesis through mevalonic acid (MVA) and methylerythritol (MEP) pathways. Genes (MVD2, HMGS, HMGR1, HMGR2, DXR, and HMGR1) encoding the primary enzymes HMGS, HMGR, DXR, and MVD in the MVA and MEP pathways were significantly upregulated in the N0-treated P. notoginseng. The saponin biosynthesis genes DDS, DDS, CYP716A52, CYP716A47, UGT74AE2, and FPS were upregulated in the N-deficient plants. Upregulation of genes involved in saponin biosynthesis promotes the accumulation of triterpenoid saponins in the N0-grown P. notoginseng.

CONCLUSIONS

N deficiency enhances primary metabolisms, such as amino acids and sugar accumulation, laying the foundation for the synthesis of flavonoids and triterpenoid saponins in P. notoginseng. F3H, DDS, FPS, HMGR, HMGS and UGT74AE2 can be considered as candidates for functional characterisation of the N-regulated accumulation of triterpenoid saponins and flavonoids in future.

A review on marine source as anticancer agents

This review investigates the potential of natural compounds obtained from marine sources for the treatment of cancer. The oceans are believed to contain physiologically active compounds, such as alkaloids, nucleosides, macrolides, and polyketides, which have shown promising effects in slowing human tumor cells both in vivo and in vitro. Various marine species, including algae, mollusks, actinomycetes, fungi, sponges, and soft corals, have been studied for their bioactive metabolites with diverse chemical structures. The review explores the therapeutic potential of various marine-derived substances and discusses their possible applications in cancer treatment.

Untargeted metabolomics in Anectocillus roxburghii with habitat heterogeneity and the key abiotic factors affecting its active ingredients

Introduction

Anoectochilus roxburghii is a rare, endangered herb with diverse pharmacological properties. Understanding the main metabolite types and characteristics of wild A. roxburghii is important for efficiently utilizing resources and examining quality according to origin.

Methods

Samples were collected from the main production areas across five regions in Fujian Province, China. An untargeted metabolomics analysis was performed on the entire plants to explore their metabolic profiles. We utilized UPLC-MS/MS to specifically quantify eight targeted flavonoids in these samples. Subsequently, correlation analysis was conducted to investigate the relationships between the flavonoids content and both the biological characteristics and geographical features.

Results

A comprehensive analysis identified a total of 3,170 differential metabolites, with terpenoids and flavonoids being the most prevalent classes. A region-specific metabolite analysis revealed that the Yongchun (YC) region showed the highest diversity of unique metabolites, including tangeretin and oleanolic acid. Conversely, the Youxi (YX) region was found to have the smallest number of unique metabolites, with only one distinct compound identified. Further investigation through KEGG pathway enrichment analysis highlighted a significant enrichment in pathways related to flavonoid biosynthesis. Further examination of the flavonoid category showed that flavonols were the most differentially abundant. We quantified eight specific flavonoids, finding that, on average, the YX region exhibited higher levels of these compounds. Correlation analysis highlighted a significant association between flavonoids and habitat, especially temperature and humidity.

Discussion

Untargeted metabolomics via LC-MS was suitable for identifying region-specific metabolites and their influence via habitat heterogeneity. The results of this study serve as a new theoretical reference for unique markers exclusively present in a specific sample group.

A self-regulated network for dynamically balancing multiple precursors in complex biosynthetic pathways

Microbial synthesis has emerged as a promising and sustainable alternative to traditional chemical synthesis and plant extraction. However, the competition between synthetic pathways and central metabolic pathways for cellular resources may impair final production efficiency. Moreover, when the synthesis of target product requires multiple precursors from the same node, the conflicts of carbon flux have further negative impacts on yields. In this study, a self-regulated network was developed to relieve the competition of precursors in complex synthetic pathways. Using 4-hydroxycoumarin (4-HC) synthetic pathway as a proof of concept, we employed an intermediate as a trigger to dynamically rewire the metabolic flux of pyruvate and control the expression levels of genes in 4-HC synthetic pathway, achieving self-regulation of multiple precursors and enhanced titer. Transcriptomic analysis results additionally demonstrated that the gene transcriptional levels of both pyruvate kinase PykF and synthetic pathway enzyme SdgA dynamically changed according to the intermediate concentrations. Overall, our work established a self-regulated network to dynamically balance the metabolic flux of two precursors in 4-HC biosynthesis, providing insight into balancing biosynthetic pathways where multiple precursors compete and interfere with each other.

Use of 3-Deoxy-D-arabino-heptulosonic acid 7-phosphate Synthase (DAHP Synthase) to Enhance the Heterologous Biosynthesis of Diosmetin and Chrysoeriol in an Engineered Strain of Streptomyces albidoflavus

Flavonoids are a large family of polyphenolic compounds with important agro-industrial, nutraceutical, and pharmaceutical applications. Among the structural diversity found in the flavonoid family, methylated flavonoids show interesting characteristics such as greater stability and improved oral bioavailability. This work is focused on the reconstruction of the entire biosynthetic pathway of the methylated flavones diosmetin and chrysoeriol in Streptomyces albidoflavus. A total of eight different genes (TAL, 4CL, CHS, CHI, FNS1, F3'H/CPR, 3'-OMT, 4'-OMT) are necessary for the heterologous biosynthesis of these two flavonoids, and all of them have been integrated along the chromosome of the bacterial host. The biosynthesis of diosmetin and chrysoeriol has been achieved, reaching titers of 2.44 mg/L and 2.34 mg/L, respectively. Furthermore, an additional compound, putatively identified as luteolin 3',4'-dimethyl ether, was produced in both diosmetin and chrysoeriol-producing strains. With the purpose of increasing flavonoid titers, a 3-Deoxy-D-arabino-heptulosonic acid 7-phosphate synthase (DAHP synthase) from an antibiotic biosynthetic gene cluster (BGC) from Amycolatopsis balhimycina was heterologously expressed in S. albidoflavus, enhancing diosmetin and chrysoeriol production titers of 4.03 mg/L and 3.13 mg/L, which is an increase of 65% and 34%, respectively. To the best of our knowledge, this is the first report on the de novo biosynthesis of diosmetin and chrysoeriol in a heterologous host.

Applications of synthetic yeast consortia for the production of native and non-native chemicals

The application of microbial consortia is a new approach in synthetic biology. Synthetic yeast consortia, simple or complex synthetic mixed cultures, have been used for the production of various metabolites. Cooperation between the members of a consortium and cross-feeding can be applied to create stable microbial communication. These consortia can: consume a variety of substrates, perform more complex functions, produce metabolites in high titer, rate, and yield (TRY), and show higher stability during industrial fermentations. Due to the new research context of synthetic consortia, few yeasts were used to build these consortia, including Saccharomyces cerevisiae, Pichia pastoris, and Yarrowia lipolytica. Here, application of the yeasts for design of synthetic microbial consortia and their advantages and bottlenecks for effective and robust production of valuable metabolites from bioresource, including: cellulose, xylose, glycerol and so on, have been reviewed. Key trends and challenges are also discussed for the future development of synthetic yeast consortia.

Saccharomyces cerevisiae biofactory to produce naringenin using a systems biology approach and a bicistronic vector expression strategy in flavonoid production

IMPORTANCE

Flavonoids are a group of compounds generally produced by plants with proven biological activity, which have recently beeen recommended for the treatment and prevention of diseases and ailments with diverse causes. In this study, naringenin was produced in adequate amounts in yeast after in silico design. The four genes of the involved enzymes from several organisms (bacteria and plants) were multi-expressed in two vectors carrying each two genes linked by a short viral peptide sequence. The batch kinetic behavior of the product, substrate, and biomass was described at lab scale. The engineered strain might be used in a more affordable and viable bioprocess for industrial naringenin procurement.

First Natural Yeast Strain Trichosporon asahii HZ10 with Robust Flavonoid Productivity and Its Potential Biosynthetic Pathway

Flavonoids are generally thought to be essential plant natural products with diverse bioactivities and pharmacological effects. Conventional approaches for the industrial production of flavonoids through plant extraction and chemical synthesis face serious economic and environmental challenges. Searching for natural robust flavonoid-producing microorganisms satisfying green and sustainable development is one of the good alternatives. Here, a natural yeast, Trichosporon asahii HZ10, isolated from raw honeycombs, was found to accumulate 146.41 mg/L total flavonoids intracellularly. Also, T. asahii HZ10 represents a broad flavonoid metabolic profiling, covering 40 flavonoids, among which nearly half were silibinin, daidzein, and irigenin trimethyl ether, especially silibinin occupying 21.07% of the total flavonoids. This is the first flavonoid-producing natural yeast strain worldwide. Furthermore, T. asahii HZ10-derived flavonoids represent favorable antioxidant activities. Interestingly, genome mining and transcriptome analysis clearly showed that T. asahii HZ10 possibly evolves a novel flavonoid synthesis pathway for the most crucial step of flavonoid skeleton synthesis, which is different from that in plants and filamentous fungi. Therefore, our results not only enrich the diversity of the natural flavonoid biosynthesis pathway but also pave an alternative way to promote the development of a synthetic biology strategy for the microbial production of flavonoids.

Metabolic engineering strategies for naringenin production enhancement in Streptomyces albidoflavus J1074

BACKGROUND

Naringenin is an industrially relevant compound due to its multiple pharmaceutical properties as well as its central role in flavonoid biosynthesis.

RESULTS

On our way to develop Streptomyces albidoflavus J1074 as a microbial cell factory for naringenin production, we have significantly increased the yields of this flavanone by combining various metabolic engineering strategies, fermentation strategies and genome editing approaches in a stepwise manner. Specifically, we have screened different cultivation media to identify the optimal production conditions and have investigated how the additive feeding of naringenin precursors influences the production. Furthermore, we have employed genome editing strategies to remove biosynthetic gene clusters (BGCs) associated with pathways that might compete with naringenin biosynthesis for malonyl-CoA precursors. Moreover, we have expressed MatBC, coding for a malonate transporter and an enzyme responsible for the conversion of malonate into malonyl-CoA, respectively, and have duplicated the naringenin BGC, further contributing to the production improvement. By combining all of these strategies, we were able to achieve a remarkable 375-fold increase (from 0.06 mg/L to 22.47 mg/L) in naringenin titers.

CONCLUSION

This work demonstrates the influence that fermentation conditions have over the final yield of a bioactive compound of interest and highlights various bottlenecks that affect production. Once such bottlenecks are identified, different strategies can be applied to overcome them, although the efficiencies of such strategies may vary and are difficult to predict.

Molecular cloning and in silico analysis of chalcone isomerase from Polygonum minus

BACKGROUND

Chalcone isomerase (CHI; EC 5.5.1.6) is one of the key enzymes in the flavonoid biosynthetic pathway that is responsible for the intramolecular cyclization of chalcones into specific 2S-flavanones.

METHODS AND RESULTS

In this study, the open reading frame (ORF) of CHI was successfully isolated from the cDNA of Polygonum minus at 711-bp long, encoding for 236 amino acid residues, with a predicted molecular weight of 25.4 kDa. Multiple sequence alignment and phylogenetic analysis revealed that the conserved residues (Thr50, Tyr108, Asn115, and Ser192) in the cleft of CHI enzyme group active site are present in PmCHI protein sequence and classified as type I. PmCHI comprises more hydrophobic residues without a signal peptide and transmembrane helices. The three-dimensional (3D) structure of PmCHI predicted through homology modeling was validated by Ramachandran plot and Verify3D, with values within the acceptable range of a good model. PmCHI was cloned into pET-28b(+) plasmid, expressed in Escherichia coli BL21(DE3) at 16 °C and partially purified.

CONCLUSION

These findings contribute to a deeper understanding of the PmCHI protein and its potential for further characterization of its functional properties in the flavonoid biosynthetic pathway.

De novo biosynthesis of sakuranetin from glucose by engineered Saccharomyces cerevisiae

Sakuranetin is a plant-natural product, which has increasingly been utilized in cosmetic and pharmaceutical industries for its extensive anti-inflammatory, anti-tumor, and immunomodulatory effects. Sakuranetin was mostly produced by extraction technology from plants, which is limited to natural conditions and biomass supply. In this study, a de novo biosynthesis pathway of sakuranetin by engineered S. cerevisiae was constructed. After a series of heterogenous gene integration, a biosynthetic pathway of sakuranetin from glucose was successfully constructed in S. cerevisiae whose sakuranetin yield reached only 4.28 mg/L. Then, a multi-module metabolic engineering strategy was applied for improving sakuranetin yield in S. cerevisiae: (1) adjusting the copy number of sakuranetin synthesis genes, (2) removing the rate-limiting factor of aromatic amino acid pathway and optimizing the synthetic pathway of aromatic amino acids to enhance the supply of carbon flux for sakuranetin, and (3) introducing acetyl-CoA carboxylase mutants ACC1^S659A,S1157A and knocking out YPL062W to strengthen the supply of malonyl-CoA which is another synthetic precursor of sakuranetin. The resultant mutant S. cerevisiae exhibited a more than tenfold increase of sakuranetin titer (50.62 mg/L) in shaking flasks. Furthermore, the sakuranetin titer increased to 158.65 mg/L in a 1-L bioreactor. To our knowledge, it is the first report on the sakuranetin de novo synthesis from glucose in S. cerevisiae. KEY POINTS: • De novo biosynthesis of sakuranetin was constructed by engineered S. cerevisiae. • Sakuranetin production was enhanced by multi-module metabolic engineering strategy. • It is the first report on the sakuranetin de novo synthesis in S. cerevisiae.

The Classification, Molecular Structure and Biological Biosynthesis of Flavonoids, and Their Roles in Biotic and Abiotic Stresses

With the climate constantly changing, plants suffer more frequently from various abiotic and biotic stresses. However, they have evolved biosynthetic machinery to survive in stressful environmental conditions. Flavonoids are involved in a variety of biological activities in plants, which can protect plants from different biotic (plant-parasitic nematodes, fungi and bacteria) and abiotic stresses (salt stress, drought stress, UV, higher and lower temperatures). Flavonoids contain several subgroups, including anthocyanidins, flavonols, flavones, flavanols, flavanones, chalcones, dihydrochalcones and dihydroflavonols, which are widely distributed in various plants. As the pathway of flavonoid biosynthesis has been well studied, many researchers have applied transgenic technologies in order to explore the molecular mechanism of genes associated with flavonoid biosynthesis; as such, many transgenic plants have shown a higher stress tolerance through the regulation of flavonoid content. In the present review, the classification, molecular structure and biological biosynthesis of flavonoids were summarized, and the roles of flavonoids under various forms of biotic and abiotic stress in plants were also included. In addition, the effect of applying genes associated with flavonoid biosynthesis on the enhancement of plant tolerance under various biotic and abiotic stresses was also discussed.

Current advancements in systems and synthetic biology studies of Saccharomyces cerevisiae

Saccharomyces cerevisiae has a long-standing history of biotechnological applications even before the dawn of modern biotechnology. The field is undergoing accelerated advancement with the recent systems and synthetic biology approaches. In this review, we highlight the recent findings in the field with a focus on omics studies of S. cerevisiae to investigate its stress tolerance in different industries. The latest advancements in S. cerevisiae systems and synthetic biology approaches for the development of genome-scale metabolic models (GEMs) and molecular tools such as multiplex Cas9, Cas12a, Cpf1, and Csy4 genome editing tools, modular expression cassette with optimal transcription factors, promoters, and terminator libraries as well as metabolic engineering. Omics data analysis is key to the identification of exploitable native genes/proteins/pathways in S. cerevisiae with the optimization of heterologous pathway implementation and fermentation conditions. Through systems and synthetic biology, various heterologous compound productions that require non-native biosynthetic pathways in a cell factory have been established via different strategies of metabolic engineering integrated with machine learning.

Flavonoid Production: Current Trends in Plant Metabolic Engineering and De Novo Microbial Production

Flavonoids are secondary metabolites that represent a heterogeneous family of plant polyphenolic compounds. Recent research has determined that the health benefits of fruits and vegetables, as well as the therapeutic potential of medicinal plants, are based on the presence of various bioactive natural products, including a high proportion of flavonoids. With current trends in plant metabolite research, flavonoids have become the center of attention due to their significant bioactivity associated with anti-cancer, antioxidant, anti-inflammatory, and anti-microbial activities. However, the use of traditional approaches, widely associated with the production of flavonoids, including plant extraction and chemical synthesis, has not been able to establish a scalable route for large-scale production on an industrial level. The renovation of biosynthetic pathways in plants and industrially significant microbes using advanced genetic engineering tools offers substantial promise for the exploration and scalable production of flavonoids. Recently, the co-culture engineering approach has emerged to prevail over the constraints and limitations of the conventional monoculture approach by harnessing the power of two or more strains of engineered microbes to reconstruct the target biosynthetic pathway. In this review, current perspectives on the biosynthesis and metabolic engineering of flavonoids in plants have been summarized. Special emphasis is placed on the most recent developments in the microbial production of major classes of flavonoids. Finally, we describe the recent achievements in genetic engineering for the combinatorial biosynthesis of flavonoids by reconstructing synthesis pathways in microorganisms via a co-culture strategy to obtain high amounts of specific bioactive compounds.

Optimization of Pinocembrin Biosynthesis in Saccharomyces cerevisiae

The flavonoid pinocembrin and its derivatives have gained increasing interest for their benefits on human health. While pinocembrin and its derivatives can be produced in engineered Saccharomyces cerevisiae, yields remain low. Here, we describe novel strategies for improved de novo biosynthesis of pinocembrin from glucose based on overcoming existing limitations in S. cerevisiae. First, we identified cinnamic acid as an inhibitor of pinocembrin synthesis. Second, by screening for more efficient enzymes and optimizing the expression of downstream genes, we reduced cinnamic acid accumulation. Third, we addressed other limiting factors by boosting the availability of the precursor malonyl-CoA, while eliminating the undesired byproduct 2',4',6'-trihydroxy dihydrochalcone. After optimizing cultivation conditions, 80 mg/L pinocembrin was obtained in a shake flask, the highest yield reported for S. cerevisiae. Finally, we demonstrated that pinocembrin-producing strains could be further engineered to generate 25 mg/L chrysin, another interesting flavone. The strains generated in this study will facilitate the production of flavonoids through the pinocembrin biosynthetic pathway.

May phytophenolics alleviate aflatoxins-induced health challenges? A holistic insight on current landscape and future prospects

The future GCC-connected environmental risk factors expedited the progression of nCDs. Indeed, the emergence of AFs is becoming a global food security concern. AFs are lethal carcinogenic mycotoxins, causing damage to the liver, kidney, and gastrointestinal organs. Long-term exposure to AFs leads to liver cancer. Almost a variety of food commodities, crops, spices, herbaceous materials, nuts, and processed foods can be contaminated with AFs. In this regard, the primary sections of this review aim to cover influencing factors in the occurrence of AFs, the role of AFs in progression of nCDs, links between GCC/nCDs and exposure to AFs, frequency of AFs-based academic investigations, and world distribution of AFs. Next, the current trends in the application of PPs to alleviate AFs toxicity are discussed. Nearly, more than 20,000 published records indexed in scientific databases have been screened to find recent trends on AFs and application of PPs in AFs therapy. Accordingly, shifts in world climate, improper infrastructures for production/storage of food commodities, inconsistency of global polices on AFs permissible concentration in food/feed, and lack of the public awareness are accounting for a considerable proportion of AFs damages. AFs exhibited their toxic effects by triggering the progression of inflammation and oxidative/nitrosative stress, in turn, leading to the onset of nCDs. PPs could decrease AFs-associated oxidative stress, genotoxic, mutagenic, and carcinogenic effects by improving cellular antioxidant balance, regulation of signaling pathways, alleviating inflammatory responses, and modification of gene expression profile in a dose/time-reliant fashion. The administration of PPs alone displayed lower biological properties compared to co-treatment of these metabolites with AFs. This issue might highlight the therapeutic application of PPs than their preventative content. Flavonoids such as quercetin and oxidized tea phenolics, curcumin and resveratrol were the most studied anti-AFs PPs. Our literature review clearly disclosed that considering PPs in antioxidant therapies to alleviate complications of AFs requires improvement in their bioavailability, pharmacokinetics, tissue clearance, and off-target mode of action. Due to the emergencies in the elimination of AFs in food/feedstuffs, further large-scale clinical assessment of PPs to decrease the consequences of AFs is highly required.

Scale-up of an amoeba-based process for the production of the cannabinoid precursor olivetolic acid

Background

The availability of new biological platform organisms to get access to innovative products and processes is fundamental for the progress in biotechnology and bioeconomy. The amoeba Dictyostelium discoideum represents a novel host system that has recently been employed for both the discovery of new natural products and as a cell factory for the production of bioactive compounds such as phytochemicals. However, an essential parameter to evaluate the potential of a new host system is the demonstration of its scalability to allow industrial applicability. Here, we aimed to develop a bioprocess for the production of olivetolic acid, the main precursor of cannabinoids synthesized by a recently engineered D. discoideum strain.

Results

In this study, a sophisticated approach is described to scale-up an amoeba-based polyketide production process in stirred tank bioreactors. Due to the shear sensitivity of the cell wall lacking amoebae, the maximum local energy dissipation rate (ε_max) was selected as a measure for the hydromechanical stress level among different scales. By performing 1.6-L scale batch fermentations with different stress conditions, we determined a maximum tolerable ε_max of 3.9 W/kg for D. discoideum. Further, we used this parameter as scale-up criterion to develop a bioprocess for olivetolic acid production starting from a 7-L stirred tank reactor to the industrially relevant 300-L scale with a product concentration of 4.8 µg/L, a productivity of 0.04 µg/L/h and a yield of 0.56 µg/g glucose.

Conclusion

We developed a robust and reliable scale-up strategy for amoeba-based bioprocesses and evaluated its applicability for the production of the cannabinoid precursor olivetolic acid. By determining the maximum tolerable hydromechanical stress level for D. discoideum, we were able to scale-up the process from shake flasks to the 300-L stirred tank reactor without any yield reduction from cell shearing. Hence, we showed the scalability and biotechnological exploitation of amoeba-based processes that can provide a reasonable alternative to chemical syntheses or extractions of phytochemicals from plant biomass.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01943-w.

Engineered biosynthesis of plant polyketides by type III polyketide synthases in microorganisms

Plant specialized metabolites occupy unique therapeutic niches in human medicine. A large family of plant specialized metabolites, namely plant polyketides, exhibit diverse and remarkable pharmaceutical properties and thereby great biomanufacturing potential. A growing body of studies has focused on plant polyketide synthesis using plant type III polyketide synthases (PKSs), such as flavonoids, stilbenes, benzalacetones, curcuminoids, chromones, acridones, xanthones, and pyrones. Microbial expression of plant type III PKSs and related biosynthetic pathways in workhorse microorganisms, such as Saccharomyces cerevisiae, Escherichia coli, and Yarrowia lipolytica, have led to the complete biosynthesis of multiple plant polyketides, such as flavonoids and stilbenes, from simple carbohydrates using different metabolic engineering approaches. Additionally, advanced biosynthesis techniques led to the biosynthesis of novel and complex plant polyketides synthesized by diversified type III PKSs. This review will summarize efforts in the past 10 years in type III PKS-catalyzed natural product biosynthesis in microorganisms, especially the complete biosynthesis strategies and achievements.

Enhancing Flavan-3-ol Biosynthesis in Saccharomyces cerevisiae

Flavan-3-ols are a group of flavonoids that exert beneficial effects. This study aimed to enhance key metabolic processes related to flavan-3-ols biosynthesis. The engineered Saccharomyces cerevisiae strain E32 that produces naringenin from glucose was further engineered for de novo production of two basic flavan-3-ols, afzelechin (AFZ) and catechin (CAT). Through introduction of flavonoid 3-hydroxylase, flavonoid 3'-hydroxylase, dihydroflavonol 4-reductase (DFR), and leucoanthocyanidin reductase (LAR), de novo production of AFZ and CAT can be achieved. The combination of FaDFR from Fragaria × ananassa and VvLAR from Vitis vinifera was optimal. (GGGGS)₂ and (EAAAK)₂ linkers between DFR and LAR proved optimal for the production of AFZ and CAT, respectively. Optimization of promoters and the enhanced supply of NADPH further increased the production. By combining the best engineering strategies, the optimum strains produced 500.5 mg/L AFZ and 321.3 mg/L CAT, respectively, after fermentation for 90 h in a 5 L bioreactor. The strategies presented could be applied for a more efficient production of flavan-3-ols by various microorganisms.

Potential of Producing Flavonoids Using Cyanobacteria As a Sustainable Chassis

Numerous plant secondary metabolites have remarkable impacts on both food supplements and pharmaceuticals for human health improvement. However, higher plants can only generate small amounts of these chemicals with specific temporal and spatial arrangements, which are unable to satisfy the expanding market demands. Cyanobacteria can directly utilize CO₂, light energy, and inorganic nutrients to synthesize versatile plant-specific photosynthetic intermediates and organic compounds in large-scale photobioreactors with outstanding economic merit. Thus, they have been rapidly developed as a "green" chassis for the synthesis of bioproducts. Flavonoids, chemical compounds based on aromatic amino acids, are considered to be indispensable components in a variety of nutraceutical, pharmaceutical, and cosmetic applications. In contrast to heterotrophic metabolic engineering pioneers, such as yeast and Escherichia coli, information about the biosynthesis flavonoids and their derivatives is less comprehensive than that of their photosynthetic counterparts. Here, we review both benefits and challenges to promote cyanobacterial cell factories for flavonoid biosynthesis. With increasing concerns about global environmental issues and food security, we are confident that energy self-supporting cyanobacteria will attract increasing attention for the generation of different kinds of bioproducts. We hope that the work presented here will serve as an index and encourage more scientists to join in the relevant research area.

Metabolic Engineering of Microbial Cell Factories for Biosynthesis of Flavonoids: A Review

Flavonoids belong to a class of plant secondary metabolites that have a polyphenol structure. Flavonoids show extensive biological activity, such as antioxidative, anti-inflammatory, anti-mutagenic, anti-cancer, and antibacterial properties, so they are widely used in the food, pharmaceutical, and nutraceutical industries. However, traditional sources of flavonoids are no longer sufficient to meet current demands. In recent years, with the clarification of the biosynthetic pathway of flavonoids and the development of synthetic biology, it has become possible to use synthetic metabolic engineering methods with microorganisms as hosts to produce flavonoids. This article mainly reviews the biosynthetic pathways of flavonoids and the development of microbial expression systems for the production of flavonoids in order to provide a useful reference for further research on synthetic metabolic engineering of flavonoids. Meanwhile, the application of co-culture systems in the biosynthesis of flavonoids is emphasized in this review.

De novo biosynthesis of garbanzol and fustin in Streptomyces albus based on a potential flavanone 3-hydroxylase with 2-hydroxylase side activity

Flavonoids are important plant secondary metabolites, which were shown to have antioxidant, anti-inflammatory or antiviral activities. Heterologous production of flavonoids in engineered microbial cell factories is an interesting alternative to their purification from plant material representing the natural source. The use of engineered bacteria allows to produce specific compounds, independent of soil, climatic or other plant-associated production parameters. The initial objective of this study was to achieve an engineered production of two interesting flavanonols, garbanzol and fustin, using Streptomyces albus as the production host. Unexpectedly, the engineered strain produced several flavones and flavonols in the absence of the additional expression of a flavone synthase (FNS) or flavonol synthase (FLS) gene. It turned out that the heterologous flavanone 3-hydroxylase (F3H) has a 2-hydroxylase side activity, which explains the observed production of 7,4'-dihydroxyflavone, resokaempferol, kaempferol and apigenin, as well as the biosynthesis of the extremely rare 2-hydroxylated intermediates 2-hydroxyliquiritigenin, 2-hydroxynaringenin and probably licodione. Other related metabolites, such as quercetin, dihydroquercetin and eriodictyol, have also been detected in culture extracts of this recombinant strain. Hence, the enzymatic versatility of S. albus can be conveniently exploited for the heterologous production of a large diversity of plant metabolites of the flavonoid family.

Bioproduction process of natural products and biopharmaceuticals: Biotechnological aspects

Decades of research have been put in place for developing sustainable routes of bioproduction of high commercial value natural products (NPs) on the global market. In the last few years alone, we have witnessed significant advances in the biotechnological production of NPs. The development of new methodologies has resulted in a better understanding of the metabolic flux within the organisms, which have driven manipulations to improve production of the target product. This was further realised due to the recent advances in the omics technologies such as genomics, transcriptomics, proteomics, metabolomics and secretomics, as well as systems and synthetic biology. Additionally, the combined application of novel engineering strategies has made possible avenues for enhancing the yield of these products in an efficient and economical way. Invention of high-throughput technologies such as next generation sequencing (NGS) and toolkits for genome editing Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated 9 (CRISPR/Cas9) have been the game changers and provided unprecedented opportunities to generate rationally designed synthetic circuits which can produce complex molecules. This review covers recent advances in the engineering of various hosts for the production of bioactive NPs and biopharmaceuticals. It also highlights general approaches and strategies to improve their biosynthesis with higher yields in a perspective of plants and microbes (bacteria, yeast and filamentous fungi). Although there are numerous reviews covering this topic on a selected species at a time, our approach herein is to give a comprehensive understanding about state-of-art technologies in different platforms of organisms.

Flavonoids from Marine-Derived Actinobacteria as Anticancer Drugs

Flavonoids represent a large diverse group of natural products that are used as a traditional medicine against various infectious diseases. They possess many biological activities including antimicrobial, antioxidant, anti-inflammatory, anti-cancer and anti-diabetic activities. Commercially, flavonoids are mainly obtained from plants, however, several challenges are faced during their extraction. Microorganisms have been known as natural sources of a wide range of bioactive compounds including flavonoids. Actinobacteria are the most prolific group of microorganisms for the production of bioactive secondary metabolites, thus facilitating the production of flavonoids. The screening programs for bioactive compounds revealed the potential application of actinobacteria to produce flavonoids with interesting biological activities, especially anticancer activities. Since marine actinobacteria are recognized as a potential source of novel anticancer agents, they are highly expected to be potential producers of anticancer flavonoids with unusual structures and properties. In this review, we highlight the production of flavonoids by actinobacteria through classical fermentation, engineering of plant biosynthetic genes in a recombinant actinobacterium and the de novo biosynthesis approach. Through these approaches, we can control and improve the production of interesting flavonoids or their derivatives for the treatment of cancer.

De Novo Biosynthesis of Multiple Pinocembrin Derivatives in Saccharomyces cerevisiae

Pinocembrin derived flavones are the major bioactive compounds presented in the Lamiaceae plants that have long been of interest due to their great pharmaceutical and economical significance. Modifications on the central skeleton of the flavone moiety have a huge impact on their biological activities. However, the enzymes responsible for structure modification of most flavones are either inefficient or remain unidentified. By integrating omics analysis of Scutellaria barbata and synthetic biology tools in yeast chassis, we characterized a novel gene encoding flavone 7-O-methyltransferase (F7OMT) and discovered a new flavone 8-hydroxylase (F8H) with increased activity. We also identified a series of flavone 6-hydroxylases (F6Hs) and flavone 8-O-methyltransferases (F8OMTs) in this study. Subsequently, we constructed the biosynthetic pathway for chrysin production by assembling catalytic elements from different species and improved the titer to 10.06 mg/L. Using the established chrysin production platform, we achieved the de novo biosynthesis of baicalein, baicalin, norwogonin, wogonin, isowogonin, and moslosooflavone in yeast. Our results indicated that the combination of omics and synthetic biology can greatly speed up the efficiency of gene mining in plants and the engineered yeasts established an alternative way for the production of pinocembrin derivatives.

Metabolic Engineering of Microorganisms for the Production of Flavonoids

Flavonoids are a class of secondary metabolites found in plant and fungus. They have been widely used in food, pharmaceutical, and nutraceutical industries owing to their significant biological activities, such as antiaging, antioxidant, anti-inflammatory, and anticancer. However, the traditional approaches for the production of flavonoids including chemical synthesis and plant extraction involved hazardous materials and complicated processes and also suffered from low product titer and yield. Microbial synthesis of flavonoids from renewable biomass such as glucose and xylose has been considered as a sustainable and environmentally friendly method for large-scale production of flavonoids. Recently, construction of microbial cell factories for efficient biosynthesis of flavonoids has gained much attention. In this article, we summarize the recent advances in microbial synthesis of flavonoids including flavanones, flavones, isoflavones, flavonols, flavanols, and anthocyanins. We put emphasis on developing pathway construction and optimization strategies to biosynthesize flavonoids and to improve their titer and yield. Then, we discuss the current challenges and future perspectives on successful strain development for large-scale production of flavonoids in an industrial level.

Transglycosylation toward naringenin-7-O-glucoside using an N180H mutant of Coprinopsis cinerea endo-β-N-acetylglucosaminidase

Flavonoids are generally glycosylated, and the glycan moieties of flavonoid glycosides are known to greatly affect their physicochemical and biological properties. Thus, the development of a variety of tools for glycan remodeling of flavonoid glycosides is highly desired. An endo-β-N-acetylglucosaminidase mutant Endo-CC N180H, which is developed as an excellent chemoenzymatic tool for creating sialylglycoproteins, was employed for the glycosylation of flavonoids. Endo-CC N180H transferred the sialyl biantennary glycans from the sialylglyco peptide to pNP-GlcNAc and narigenin-7-O-glucoside. The kinetic parameters of Endo-CC N180H towards SGP and pNP-GlcNAc were determined. Flavonoid glucosides harboring a 1,3-diol structure in the glucose moieties acted as substrates of Endo-CC N180H. We proposed that the sialyl biantennary glycan transfer to the flavonoid by Endo-CC N180H could pave the way for the improvement of the inherent biological functions of the flavonoids and creation of novel flavonoid glycoside derivatives for future human health benefits including foods and drugs.

Rational Design of Flavonoid Production Routes Using Combinatorial and Precursor-Directed Biosynthesis

Combinatorial biosynthesis has great potential for designing synthetic circuits and amplifying the production of new active compounds. Studies on multienzyme cascades are extremely useful for improving our knowledge on enzymatic catalysis. In particular, the elucidation of enzyme substrate promiscuity can be potentially used for bioretrosynthetic approaches, leading to the design of alternative and more convenient routes to produce relevant molecules. In this perspective, plant-derived polyketides are extremely adaptable to those synthetic biological applications. Here, we present a combination of an in vitro CoA ligase activity assay coupled with a bacterial multigene expression system that leads to precursor-directed biosynthesis of 21 flavonoid derivatives. When the vast knowledge from protein databases is exploited, the herein presented procedure can be easily repeated with additional plant-derived polyketides. Lastly, we report an efficient in vivo expression system that can be further exploited to heterologously express pathways not necessarily related to plant polyketide synthases.