Biosynthesis of resveratrol by an endophytic Priestia megaterium PH3 via the phenylpropane pathway

Resveratrol (RES) is a secondary metabolite synthesized by plants in response to environmental stress and pathogen infection, which is of great significance for the industrial production of RES by fermentation culture. In this study, we aimed to explore the biosynthesis pathway of RES and its key enzymes in the Priestia megaterium PH3, which was isolated and screened from peanut fruit. Through Liquid Chromatography-Mass Spectrometry (LC-MS) analysis, we quantified the RES content and distribution in the culture medium and determined that Priestia megaterium PH3 mainly secreted RES extracellularly. Furthermore, the highest production of RES was observed in YPD, yielding an impressive 127.46 ± 6.11 μg/L. By optimizing the fermentation conditions, we achieved a remarkable RES yield of 946.82 ± 24.74 μg/L within just 2 days, which represents the highest reported yield for a natural isolate produced in such a short time frame. Our investigation revealed that the phenylpropane pathway is responsible for RES synthesis in this bacterium, with cinnamate 4-hydroxylase (C4H) identified as the main rate-limiting enzyme. Overall, our findings highlight the robust RES production capabilities of Priestia megaterium PH3, offering novel insights and potential applications for bacterial fermentation in RES production. KEY POINTS: • RES synthesized by the bacterium was confirmed through the phenylpropane pathway. • The key rate-limiting enzyme for biosynthesis-RES is C4H. • RES reached 946.82 ± 24.74 μg/L after fermentation for 2 days.

Microbial production of nutraceuticals: Metabolic engineering interventions in phenolic compounds, poly unsaturated fatty acids and carotenoids synthesis

Nutraceuticals have attained substantial attention due to their health-boosting or disease-prevention characteristics. Growing awareness about the potential of nutraceuticals for the prevention and management of diseases affecting human has led to an increase in the market value of nutraceuticals in several billion dollars. Nevertheless, limitations in supply and isolation complications from plants, animals or fungi, limit the large-scale production of nutraceuticals. Microbial engineering at metabolic level has been proved as an environment friendly substitute for the chemical synthesis of nutraceuticals. Extensively used microbial systems such as E. coli and S. cerevisiae have been modified as versatile cell factories for the synthesis of diverse nutraceuticals. This review describes current interventions in metabolic engineering for synthesising some of the therapeutically important nutraceuticals (phenolic compounds, polyunsaturated fatty acids and carotenoids). We focus on the interventions in enhancing product yield through engineering at gene level or pathway level.

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.

Modular engineering of E. coli coculture for efficient production of resveratrol from glucose and arabinose mixture

Resveratrol, a valuable plant-derived polyphenolic compound with various bioactivities, has been widely used in nutraceutical industries. Microbial production of resveratrol suffers from metabolic burden and low malonyl-CoA availability, which is a big challenge for synthetic biology. Herein, we took advantage of coculture engineering and divided the biosynthetic pathway of resveratrol into the upstream and downstream strains. By enhancing the supply of malonyl-CoA via CRISPRi system and fine-tuning the expression intensity of the synthetic pathway genes, we significantly improved the resveratrol productivity of the downstream strain. Furthermore, we developed a resveratrol addiction circuit that coupled the growth of the upstream strain and the resveratrol production of the downstream strain. The bidirectional interaction stabilized the coculture system and increased the production of resveratrol by 74%. Moreover, co-utilization of glucose and arabinose by the coculture system maintained the growth advantage of the downstream strain for production of resveratrol throughout the fermentation process. Under optimized conditions, the engineered E. coli coculture system produced 204.80 mg/L of resveratrol, 12.8-fold improvement over monoculture system. This study demonstrates the promising potential of coculture engineering for efficient production of natural products from biomass.

Synthetic Biology-Driven Microbial Production of Resveratrol: Advances and Perspectives

Resveratrol, a bioactive natural product found in many plants, is a secondary metabolite and has attracted much attention in the medicine and health care products fields due to its remarkable biological activities including anti-cancer, anti-oxidation, anti-aging, anti-inflammation, neuroprotection and anti-glycation. However, traditional chemical synthesis and plant extraction methods are impractical for industrial resveratrol production because of low yield, toxic chemical solvents and environmental pollution during the production process. Recently, the biosynthesis of resveratrol by constructing microbial cell factories has attracted much attention, because it provides a safe and efficient route for the resveratrol production. This review discusses the physiological functions and market applications of resveratrol. In addition, recent significant biotechnology advances in resveratrol biosynthesis are systematically summarized. Furthermore, we discuss the current challenges and future prospects for strain development for large-scale resveratrol production at an industrial level.

Enhanced Production of Pterostilbene in Escherichia coli Through Directed Evolution and Host Strain Engineering

Pterostilbene is a derivative of resveratrol with a higher bioavailability and biological activity, which shows antioxidant, anti-inflammatory, antitumor, and antiaging activities. Here, directed evolution and host strain engineering were used to improve the production of pterostilbene in Escherichia coli. First, the heterologous biosynthetic pathway enzymes of pterostilbene, including tyrosine ammonia lyase, p-coumarate: CoA ligase, stilbene synthase, and resveratrol O-methyltransferase, were successively directly evolved through error-prone polymerase chain reaction (PCR). Four mutant enzymes with higher activities of in vivo and in vitro were obtained. The directed evolution of the pathway enzymes increased the pterostilbene production by 13.7-fold. Then, a biosensor-guided genome shuffling strategy was used to improve the availability of the precursor L-tyrosine of the host strain E. coli TYR-30 used for the production of pterostilbene. A shuffled E. coli strain with higher L-tyrosine production was obtained. The shuffled strain harboring the evolved pathway produced 80.04 ± 5.58 mg/l pterostilbene, which is about 2.3-fold the highest titer reported in literatures.

Elimination of aromatic fusel alcohols as by-products of Saccharomyces cerevisiae strains engineered for phenylpropanoid production by 2-oxo-acid decarboxylase replacement

Engineered strains of the yeast Saccharomyces cerevisiae are intensively studied as production platforms for aromatic compounds such as hydroxycinnamic acids, stilbenoids and flavonoids. Heterologous pathways for production of these compounds use l-phenylalanine and/or l-tyrosine, generated by the yeast shikimate pathway, as aromatic precursors. The Ehrlich pathway converts these precursors to aromatic fusel alcohols and acids, which are undesirable by-products of yeast strains engineered for production of high-value aromatic compounds. Activity of the Ehrlich pathway requires any of four S. cerevisiae 2-oxo-acid decarboxylases (2-OADCs): Aro10 or the pyruvate-decarboxylase isoenzymes Pdc1, Pdc5, and Pdc6. Elimination of pyruvate-decarboxylase activity from S. cerevisiae is not straightforward as it plays a key role in cytosolic acetyl-CoA biosynthesis during growth on glucose. In a search for pyruvate decarboxylases that do not decarboxylate aromatic 2-oxo acids, eleven yeast and bacterial 2-OADC-encoding genes were investigated. Homologs from Kluyveromyces lactis (KlPDC1), Kluyveromyces marxianus (KmPDC1), Yarrowia lipolytica (YlPDC1), Zymomonas mobilis (Zmpdc1) and Gluconacetobacter diazotrophicus (Gdpdc1.2 and Gdpdc1.3) complemented a Pdc⁻ strain of S. cerevisiae for growth on glucose. Enzyme-activity assays in cell extracts showed that these genes encoded active pyruvate decarboxylases with different substrate specificities. In these in vitro assays, ZmPdc1, GdPdc1.2 or GdPdc1.3 had no substrate specificity towards phenylpyruvate. Replacing Aro10 and Pdc1,5,6 by these bacterial decarboxylases completely eliminated aromatic fusel-alcohol production in glucose-grown batch cultures of an engineered coumaric acid-producing S. cerevisiae strain. These results outline a strategy to prevent formation of an important class of by-products in ‘chassis’ yeast strains for production of non-native aromatic compounds.

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Identification of pyruvate decarboxylases active with pyruvate but not with aromatic 2-oxo acids.

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Zymomonas mobilis pyruvate decarboxylase can replace the native yeast enzymes.

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Expression of Z. mobilis pyruvate decarboxylase removes formation of fusel alcohols.

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Elimination of fusel alcohol by products improves formation of coumaric acid.

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Decarboxylase swapping is a beneficial strategy for production of non-native aromatics.

The Semi-Supervised Strategy of Machine Learning on the Gene Family Diversity to Unravel Resveratrol Synthesis

Resveratrol is a phytochemical with medicinal benefits, being well-known for its presence in wine. Plants develop resveratrol in response to stresses such as pathogen infection, UV radiation, and other mechanical stress. The recent publications of genomic sequences of resveratrol-producing plants such as grape, peanut, and eucalyptus can expand our molecular understanding of resveratrol synthesis. Based on a gene family count matrix of Viridiplantae members, we uncovered important gene families that are common in resveratrol-producing plants. These gene families could be prospective candidates for improving the efficiency of synthetic biotechnology-based artificial resveratrol manufacturing.

Recent Advances in Metabolically Engineered Microorganisms for the Production of Aromatic Chemicals Derived From Aromatic Amino Acids

Aromatic compounds derived from aromatic amino acids are an important class of diverse chemicals with a wide range of industrial and commercial applications. They are currently produced via petrochemical processes, which are not sustainable and eco-friendly. In the past decades, significant progress has been made in the construction of microbial cell factories capable of effectively converting renewable carbon sources into value-added aromatics. Here, we systematically and comprehensively review the recent advancements in metabolic engineering and synthetic biology in the microbial production of aromatic amino acid derivatives, stilbenes, and benzylisoquinoline alkaloids. The future outlook concerning the engineering of microbial cell factories for the production of aromatic compounds is also discussed.

Investigating E. coli Coculture for Resveratrol Production with 13C Metabolic Flux Analysis

Resveratrol, a phytoalexin produced by plants, has several beneficial effects in humans. It can be produced using Escherichia coli by introducing only three heterologous genes: TAL, 4CL, and STS. However, the resveratrol synthesis pathway requires two precursors, tyrosine and acetyl-CoA, which are produced by two branched central metabolic pathways. Therefore, overexpression of these genes in E. coli results in the production of only trace amounts of resveratrol. In this study, we attempted to produce resveratrol via coculture of two engineered strains in which the two metabolic pathways are activated. The first strain was engineered to produce p-coumaric acid using tyrosine as a precursor, which can be synthesized by the pentose phosphate pathway. The second strain produced resveratrol by combining p-coumaric acid from the first strain and malonyl-CoA synthesized from acetyl-CoA, which is produced by the glycolytic pathway. In total, 55.7 mg/L of resveratrol was produced from 20 g/L of glucose via coculture of these two strains in glucose minimal medium without any supplements. The metabolic fluxes in each of the strains producing resveratrol were successfully investigated by ¹³C metabolic flux analysis. The results showed that the balance between the citric acid cycle and the malonyl-CoA supply node was important for resveratrol production.

Biotechnological Advances in Resveratrol Production and its Chemical Diversity

The very well-known bioactive natural product, resveratrol (3,5,4'-trihydroxystilbene), is a highly studied secondary metabolite produced by several plants, particularly grapes, passion fruit, white tea, and berries. It is in high demand not only because of its wide range of biological activities against various kinds of cardiovascular and nerve-related diseases, but also as important ingredients in pharmaceuticals and nutritional supplements. Due to its very low content in plants, multi-step isolation and purification processes, and environmental and chemical hazards issues, resveratrol extraction from plants is difficult, time consuming, impracticable, and unsustainable. Therefore, microbial hosts, such as Escherichia coli, Saccharomyces cerevisiae, and Corynebacterium glutamicum, are commonly used as an alternative production source by improvising resveratrol biosynthetic genes in them. The biosynthesis genes are rewired applying combinatorial biosynthetic systems, including metabolic engineering and synthetic biology, while optimizing the various production processes. The native biosynthesis of resveratrol is not present in microbes, which are easy to manipulate genetically, so the use of microbial hosts is increasing these days. This review will mainly focus on the recent biotechnological advances for the production of resveratrol, including the various strategies used to produce its chemically diverse derivatives.

An Expanded Synthetic Biology Toolkit for Gene Expression Control in Acetobacteraceae

The availability of different host chassis will greatly expand the range of applications in synthetic biology. Members of the Acetobacteraceae family of Gram-negative bacteria form an attractive class of nonmodel microorganisms that can be exploited to produce industrial chemicals, food and beverage, and biomaterials. One such biomaterial is bacterial cellulose, which is a strong and ultrapure natural polymer used in tissue engineering scaffolds, wound dressings, electronics, food additives, and other products. However, despite the potential of Acetobacteraceae in biotechnology, there has been considerably little effort to fundamentally reprogram the bacteria for enhanced performance. One limiting factor is the lack of a well-characterized, comprehensive toolkit to control expression of genes in biosynthetic pathways and regulatory networks to optimize production and cell viability. Here, we address this shortcoming by building an expanded genetic toolkit for synthetic biology applications in Acetobacteraceae. We characterized the performance of multiple natural and synthetic promoters, ribosome binding sites, terminators, and degradation tags in three different strains, namely, Gluconacetobacter xylinus ATCC 700178, Gluconacetobacter hansenii ATCC 53582, and Komagataeibacter rhaeticus iGEM. Our quantitative data revealed strain-specific and common design rules for the precise control of gene expression in these industrially relevant bacterial species. We further applied our tools to synthesize a biodegradable cellulose-chitin copolymer, adjust the structure of the cellulose film produced, and implement CRISPR interference for ready down-regulation of gene expression. Collectively, our genetic parts will enable the efficient engineering of Acetobacteraceae bacteria for the biomanufacturing of cellulose-based materials and other commercially valuable products.

Production of methylparaben in Escherichia coli

Since the 1930s, parabens have been employed widely as preservatives in food, pharmaceutical, and personal care products. These alkyl esters of benzoic acid occur naturally in a broad range of plant species, where they are thought to enhance overall fitness through disease resistance and allelopathy. Current manufacture of parabens relies on chemical synthesis and the processing of 4-hydroxybenzoate as a precursor. A variety of bio-based production platforms have targeted 4-hydroxybenzoate for a greener alternative to chemical manufacturing, but parabens have yet to be made in microbes. Here, we deploy the plant enzyme benzoic acid carboxyl methyltransferase together with four additional recombinant enzymes to produce methylparaben in Escherichia coli. The feasibility of a tyrosine-dependent route to methylparaben is explored, establishing a framework for linking paraben production to emerging high-tyrosine E. coli strains. However, our use of a unique plant enzyme for bio-based methylparaben biosynthesis is potentially applicable to any microbial system engineered for the manufacture of 4-hydroxybenzoate.

Combinatorial Optimization of Resveratrol Production in Engineered E. coli

Resveratrol, a plant-derived polyphenolic compound with various health activities, is widely used in nutraceutical and food additives. Herein, combinatorial optimization of resveratrol biosynthetic pathway and intracellular environment of E. coli was carried out. By screening pathway genes from various species and exploring their expression pattern, we initially constructed resveratrol-producing strains. Further targeting at availability of malonyl-CoA through expressing ACC of Corynebacterium glutamicum and antisense inhibiting native fabD significantly increased resveratrol biosynthesis. Transport engineering for resveratrol secretion and molecular chaperones helping for folding heterologous enzymes were employed to improve the intracellular environments in remarkable degrees. By introducing PcTAL of Phanerochaete chrysosporium and tuning expression model of PcTAL, At4CL, and VvSTS, an engineered E. coli produced 57.77 mg/L of resveratrol from l-tyrosine. After integrating the above strategies, resveratrol titer reached to 238.71 mg/L from l-tyrosine. The combinatorial optimization in this study provides a promising strategy to produce valuable natural products in heterologous expression systems.

Engineering stilbene metabolic pathways in microbial cells

Numerous in vitro and in vivo studies on biological activities of phytostilbenes have brought to the fore the remarkable properties of these compounds and their derivatives, making them a top storyline in natural product research fields. However, getting stilbenes in sufficient amounts for routine biological activity studies and make them available for pharmaceutical and/or nutraceutical industry applications, is hampered by the difficulty to source them through synthetic chemistry-based pathways or extraction from the native plants. Hence, microbial cell cultures have rapidly became potent workhorse factories for stilbene production. In this review, we present the combined efforts made during the past 15 years to engineer stilbene metabolic pathways in microbial cells, mainly the Saccharomyces cerevisiae baker yeast, the Escherichia coli and the Corynebacterium glutamicum bacteria. Rationalized approaches to the heterologous expression of the partial or the entire stilbene biosynthetic routes are presented to allow the identification and/or bypassing of the major bottlenecks in the endogenous microbial cell metabolism as well as potential regulations of the genes involved in these metabolic pathways. The contributions of bioinformatics to synthetic biology are developed to highlight their tremendous help in predicting which target genes are likely to be up-regulated or deleted for controlling the dynamics of precursor flows in the tailored microbial cells. Further insight is given to the metabolic engineering of microbial cells with "decorating" enzymes, such as methyl and glycosyltransferases or hydroxylases, which can act sequentially on the stilbene core structure. Altogether, the cellular optimization of stilbene biosynthetic pathways integrating more and more complex constructs up to twelve genetic modifications has led to stilbene titers ranging from hundreds of milligrams to the gram-scale yields from various carbon sources. Through this review, the microbial production of stilbenes is analyzed, stressing both the engineering dynamic regulation of biosynthetic pathways and the endogenous control of stilbene precursors.

Heterologous production of resveratrol in bacterial hosts: current status and perspectives

The polyphenol resveratrol (3,5,4'-trihydroxystilbene) is a well-known plant secondary metabolite, commonly used as a medical ingredient and a nutritional supplement. Due to its health-promoting properties, the demand for resveratrol is expected to continue growing. This stilbene can be found in different plants, including grapes, berries (blackberries, blueberries and raspberries), peanuts and their derived food products, such as wine and juice. The commercially available resveratrol is usually extracted from plants, however this procedure has several drawbacks such as low concentration of the product of interest, seasonal variation, risk of plant diseases and product stability. Alternative production processes are being developed to enable the biotechnological production of resveratrol by genetically engineering several microbial hosts, such as Escherichia coli, Corynebacterium glutamicum, Lactococcus lactis, among others. However, these bacterial species are not able to naturally synthetize resveratrol and therefore genetic modifications have been performed. The application of emerging metabolic engineering offers new possibilities for strain and process optimization. This mini-review will discuss the recent progress on resveratrol biosynthesis in engineered bacteria, with a special focus on the metabolic engineering modifications, as well as the optimization of the production process. These strategies offer new tools to overcome the limitations and challenges for microbial production of resveratrol in industry.

Resveratrol and Related Stilbenoids, Nutraceutical/Dietary Complements with Health-Promoting Actions: Industrial Production, Safety, and the Search for Mode of Action

This paper reviews the potential of stilbenoids as nutraceuticals. Stilbenoid compounds in wine are considered key factors in health-promoting benefits. Resveratrol and resveratrol-related compounds are found in a large diversity of vegetal products. The stilbene composition varies from wine to wine and from one season to another. Therefore, the article also reviews how food science and technology and wine industry may help in providing wines and/or food supplements with efficacious concentrations of stilbenes. The review also presents results from clinical trials and those derived from genomic/transcriptomic studies. The most studied stilbenoid, resveratrol, is a very safe compound. On the other hand, the potential benefits of stilbene intake are multiple and are apparently due to downregulation more than upregulation of gene expression. The field may take advantage from identifying the mechanism of action(s) and from providing useful data to show evidence for specific health benefits in a given tissue or for combating a given disease.

Efficient de novo synthesis of resveratrol by metabolically engineered Escherichia coli

Resveratrol has been the subject of numerous scientific investigations due to its health-promoting activities against a variety of diseases. However, developing feasible and efficient microbial processes remains challenging owing to the requirement of supplementing expensive phenylpropanoic precursors. Here, various metabolic engineering strategies were developed for efficient de novo biosynthesis of resveratrol. A recombinant malonate assimilation pathway from Rhizobium trifolii was introduced to increase the supply of the key precursor malonyl-CoA and simultaneously, the clustered regularly interspaced short palindromic repeats interference system was explored to down-regulate fatty acid biosynthesis pathway to inactivate the malonyl-CoA consumption pathway. Down-regulation of fabD, fabH, fabB, fabF, fabI increased resveratrol production by 80.2, 195.6, 170.3, 216.5 and 123.7%, respectively. Furthermore, the combined effect of these genetic perturbations was investigated, which increased the resveratrol titer to 188.1 mg/L. Moreover, the efficiency of this synthetic pathway was improved by optimizing the expression level of the rate-limiting enzyme TAL based on reducing mRNA structure of 5' region. This further increased the final resveratrol titer to 304.5 mg/L. The study described here paves the way to the development of a simple and economical process for microbial production of resveratrol.