Metabolic engineering of Escherichia coli for (2S)-pinocembrin production from glucose by a modular metabolic strategy

Flavonoids are valuable natural products widely used in human health and nutrition. Recent advances in synthetic biology and metabolic engineering have yielded improved strain titers and yields. However, current fermentation strategies often require supplementation of expensive phenylpropanoic precursors in the media and separate evaluation of each strategy in turn as part of the flavonoid pathway, implicitly assuming the modifications are additive. In this study, an Escherichia coli fermentation system was developed to bypass both of these problems. An eight-step pathway, consisting of 3-deoxy-d-arabinoheptulosonate-7-phosphate synthase (DAHPS), chorismate mutase/prephenate dehydratase (CM/PDT), phenylalanine ammonia lyase (PAL), 4-coumarate:CoA ligase (4CL), chalcone synthase (CHS), chalcone isomerase (CHI), malonate synthetase, and malonate carrier protein, was assembled on four vectors in order to produce the flavonoid precursor (2S)-pinocembrin directly from glucose. Furthermore, a modular metabolic strategy was employed to identify conditions that optimally balance the four pathway modules. Once this metabolic balance was achieved, such strains were capable of producing 40.02 mg/L (2S)-pinocembrin directly from glucose. These results were attained by culturing engineered cells in minimal medium without additional precursor supplementation. The fermentation platform described here paves the way for the development of an economical process for microbial production of flavonoids directly from glucose.     

大肠杆菌中从头合成白藜芦醇途径的设计及优化

白藜芦醇是一种极具药用价值的植物源芪类化合物。为了在E. coli实现白藜芦醇的从头合成,构建了由酪氨酸解氨酶（TAL）,香豆酸-CoA合成酶（4CL）和白藜芦醇合成酶（STS）组成的非天然合成途径。经3天发酵后,白藜芦醇产量仅为2.67 mg/L,而其中间体香豆酸的积累达到了95.64 mg/L。为了进一步改善异源途径的效率,对4CL和STS模块采取融合表达、高拷贝表达及启动子工程改造的策略,最终使白藜芦醇产量提高到了9.6倍,达到了25.76 mg/L,同时香豆酸的积累减少到了20.38 mg/L。这些研究结果为更高效白藜芦醇从头合成工程菌的构建及最终实现白藜芦醇的微生物大规模生产奠定了基础。     

Efficient de novo synthesis of resveratrol by metabolically engineered <Emphasis Type="Italic">Escherichia coli</Emphasis>

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.     

A novel process for obtaining pinosylvin using combinatorial bioengineering in <Emphasis Type="Italic">Escherichia coli</Emphasis>

Pinosylvin as a bioactive stilbene is of great interest for food supplements and pharmaceuticals development. In comparison to conventional extraction of pinosylvin from plant sources, biosynthesis engineering of microbial cell factories is a sustainable and flexible alternative method. Current synthetic strategies often require expensive phenylpropanoic precursor and inducer, which are not available for large-scale fermentation process. In this study, three bioengineering strategies were described to the development of a simple and economical process for pinosylvin biosynthesis in Escherichia coli. Firstly, we evaluated different construct environments to give a highly efficient constitutive system for enzymes of pinosylvin pathway expression: 4-coumarate: coenzyme A ligase (4CL) and stilbene synthase (STS). Secondly, malonyl coenzyme A (malonyl-CoA) is a key precursor of pinosylvin bioproduction and at low level in E. coli cell. Thus clustered regularly interspaced short palindromic repeats interference (CRISPRi) was explored to inactivate malonyl-CoA consumption pathway to increase its availability. The resulting pinosylvin content in engineered E. coli was obtained a 1.9-fold increase depending on the repression of fabD (encoding malonyl-CoA-ACP transacylase) gene. Eventually, a phenylalanine over-producing E. coli consisting phenylalanine ammonia lyase was introduced to produce the precursor of pinosylvin, trans-cinnamic acid, the crude extraction of cultural medium was used as supplementation for pinosylvin bioproduction. Using these combinatorial processes, 47.49 mg/L pinosylvin was produced from glycerol.     

Modular Optimization of Heterologous Pathways for De Novo Synthesis of (2S)-Naringenin in Escherichia coli

Due to increasing concerns about food safety and environmental issues, bio-based production of flavonoids from safe, inexpensive, and renewable substrates is increasingly attracting attention. Here, the complete biosynthetic pathway, consisting of 3-deoxy-D-arabinoheptulosonate 7-phosphate synthase (DAHPS), chorismate mutase/prephenate dehydrogenase (CM/PDH), tyrosine ammonia lyase (TAL), 4-coumarate:CoA ligase (4CL), chalcone synthase (CHS), chalcone isomerase (CHI), malonate synthetase, and malonate carrier protein, was constructed using pre-made modules to overproduce (2S)-naringenin from D-glucose. Modular pathway engineering strategies were applied to the production of the flavonoid precursor (2S)-naringenin from L-tyrosine to investigate the metabolic space for efficient conversion. Modular expression was combinatorially tuned by modifying plasmid gene copy numbers and promoter strengths to identify an optimally balanced pathway. Furthermore, a new modular pathway from D-glucose to L-tyrosine was assembled and re-optimized with the identified optimal modules to enable de novo synthesis of (2S)-naringenin. Once this metabolic balance was achieved, the optimum strain was capable of producing 100.64 mg/L (2S)-naringenin directly from D-glucose, which is the highest production titer from D-glucose in Escherichia coli. The fermentation system described here paves the way for the development of an economical process for microbial production of flavonoids.     

Optimization of a heterologous pathway for the production of flavonoids from glucose

The development of efficient microbial processes for the production of flavonoids has been a metabolic engineering goal for the past several years, primarily due to the purported health-promoting effects of these compounds. Although significant strides have been made recently in improving strain titers and yields, current fermentation strategies suffer from two major drawbacks-(1) the requirement for expensive phenylpropanoic precursors supplemented into the media and (2) the need for two separate media formulations for biomass/protein generation and flavonoid production. In this study, we detail the construction of a series of strains capable of bypassing both of these problems. A four-step heterologous pathway consisting of the enzymes tyrosine ammonia lyase (TAL), 4-coumarate:CoA ligase (4CL), chalcone synthase (CHS), and chalcone isomerase (CHI) was assembled within two engineered l-tyrosine Escherichia coli overproducers in order to enable the production of the main flavonoid precursor naringenin directly from glucose. During the course of this investigation, we discovered that extensive optimization of both enzyme sources and relative gene expression levels was required to achieve high quantities of both p-coumaric acid and naringenin accumulation. Once this metabolic balance was achieved, however, such strains were found to be capable of producing 29 mg/l naringenin from glucose and up to 84 mg/l naringenin with the addition of the fatty acid enzyme inhibitor, cerulenin. These results were obtained through cultivation of E. coli in a single minimal medium formulation without additional precursor supplementation, thus paving the way for the development of a simple and economical process for the microbial production of flavonoids directly from glucose.     

Production of a major stilbene phytoalexin, resveratrol in peanut (Arachis hypogaea) and peanut products: a mini review

As a major stilbene phytoalexin, resveratrol is produced or elicited in several plant species as a part of defense systems protecting plants against diseases. Resveratrol can be present in both the trans- and cis-isomeric forms, and only the trans-form increases the life expectancy and lowers the risk of cardiovascular diseases as the most bioactive form. In addition to the usages for diet and industry, peanut plant (Arachis hypogaea) and peanuts are getting higher attention due to their containment of resveratrol in the kernels and other parts of peanut plant, such as leaves, roots, and peanut shell. Recently, natural resveratrol derived from peanuts has also become a promising nutraceutical agent, promoting human health. Resveratrol has also been detected in peanut products including peanut butters, roasted peanuts, and boiled peanuts. Although, smaller and immature peanuts contain higher levels of resveratrol than mature peanuts, resveratrol in peanuts can also be preserved by cooking or manufacturing processes. Moreover, the amount of resveratrol in peanut plants and peanuts has been found to increase by external stimuli including microbial infection, wounding, UV light irradiation, ultrasonication, yeast extract treatment and by plant stress hormones. In addition, molecular level analysis has confirmed that four resveratrol synthase (RS) genes (RS1, RS2, RS3 and RS4) which catalyze synthesis of resveratrol have been identified in peanuts, and up-regulation of the genes is positively correlated to the increased contents of resveratrol. In this review, we summarize the natural biosynthesis of resveratrol in peanuts and peanut plants, as well as the occurrence of this natural phytoalexin in various peanut products. A brief knowledge on the biosynthetic pathway of resveratrol synthesis has been described. This review also deals on highlighting the effect of various external stimuli (biotic and abiotic stresses) in order to achieve the maximum induction and/or elicitation of resveratrol in peanuts and peanut plants.     

Biotechnological production of l-tyrosine and derived compounds

The aromatic amino acid l-tyrosine is a compound with multiple applications in the food, pharmaceutical, cosmetic and chemical industries. This review summarizes the current knowledge on the metabolic pathways involved in the synthesis of this amino acid and the strategies employed to develop and improve microbial production strains. Common strategies for l-tyrosine overproduction include the elimination of negative feedback control in key pathway enzymes and increasing the pool of the aromatic precursors phosphoenolpyruvate and erythrose-4-phosphate. Following these approaches, production strains have been generated that allow the synthesis of l-tyrosine with a yield from glucose corresponding to 80% of the theoretical maximum. Recent developments in the utilization of l-tyrosine as a substrate for microbial and enzymatic conversion into valuable products are also presented and discussed. For example, the production of the aromatic polymer melanin has been reported by the bioconversion of l-tyrosine using an Escherichia coli strain expressing a gene encoding the enzyme tyrosinase from Rhizobium etli. Metabolic engineering by expressing genes encoding the enzyme p-hydroxyphenylacetate 3-hydroxylase in an E. coli strain modified for l-tyrosine production from glucose results in the capacity to synthesize l-3,4-dihydroxyphenylalanine, a compound employed for treating Parkinson's disease.     

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.     

Production of resveratrol from tyrosine in metabolically engineered Saccharomyces cerevisiae

Resveratrol, a polyphenol compound found in grape skins, has been proposed to account for the beneficial effects of red wine against heart disease. To produce resveratrol in Saccharomyces cerevisiae, four heterologous genes were introduced: the phenylalanine ammonia lyase gene from Rhodosporidium toruloides, the cinnamic acid 4-hydroxylase and 4-coumarate:coenzyme A ligase genes both from Arabidopsis thaliana, and the stilbene synthase gene from Arachis hypogaea. When this recombinant yeast was cultivated by batch fermentation in YP medium containing 2% galactose, it produced 2.6mg/L p-coumaric acid and 3.3mg/L resveratrol. In order to increase the pool of malonyl-CoA, a key precursor in resveratrol biosynthesis, the acetyl-CoA carboxylase (ACC1) gene was additionally overexpressed in the yeast by replacing the native promoter of the ACC1 gene with the stronger GAL1 promoter and this resulted in enhanced production of resveratrol (4.3mg/L). Furthermore, when tyrosine was supplemented in the medium, the concentration of resveratrol increased up to 5.8mg/L. This result illustrates a possible strategy for developing metabolically engineered yeast strain for the economical production of resveratrol from cheap amino acids.     

Substrate specificity in vivo and in vitro in the formation of stilbenes. Biosynthesis of rhaponticin

The biosynthesis of the stilbene glucoside rhaponticin (3,5,3′-trihydroxy-4′-methoxystilbene 3-O-β-d-glucoside), a constituent of rhubarb (Rheum rhaponticum), was localized in the rhizome. Acetate and various phenylpropane derivatives were tested as precursors in feeding experiments. p-Coumaric acid was more efficiently incorporated than isoferulic acid, resveratrol (3,5,4′-trihydroxystilbene) was found to be the best precursor of rhaponticin. In vitro, for the stilbene-synthesizing system an even higher selectivity in favor of the p-hydroxy compound was observed. When various cinnamoyl-CoA derivatives were tested, membrane-bound enzyme preparations from rhizome converted at pH 7.5p-coumaroyl-CoA into resveratrol whereas rhapontigenin was not formed from isoferuloyl-CoA. Caffeoyl-CoA was converted to astringenin, but with lower rates and at a more acidic pH. The stilbene skeleton is, therefore, synthesized from a phenylpropane moiety carrying a 4′-hydroxysubstitution, while further derivatization to the 3′-hydroxy-4′-methoxy structure takes place at the level of stilbenes.     

Metabolic engineering of Saccharomyces cerevisiae for the synthesis of the wine-related antioxidant resveratrol

The stilbene resveratrol is a stress metabolite produced by Vitis vinifera grapevines during fungal infection, wounding or UV radiation. Resveratrol is synthesised particularly in the skins of grape berries and only trace amounts are present in the fruit flesh. Red wine contains a much higher resveratrol concentration than white wine, due to skin contact during fermentation. Apart from its antifungal characteristics, resveratrol has also been shown to have cancer chemopreventive activity and to reduce the risk of coronary heart disease. It acts as an antioxidant and anti-mutagen and has the ability to induce specific enzymes that metabolise carcinogenic substances. The objective of this pilot study was to investigate the feasibility of developing wine yeasts with the ability to produce resveratrol during fermentation in both red and white wines, thereby increasing the wholesomeness of the product. To achieve this goal, the phenylpropanoid pathway in Saccharomyces cerevisiae would have to be introduced to produce p-coumaroyl-CoA, one of the substrates required for resveratrol synthesis. The other substrate for resveratrol synthase, malonyl-CoA, is already found in yeast and is involved in de novo fatty-acid biosynthesis. We hypothesised that production of p-coumaroyl-CoA and resveratrol can be achieved by co-expressing the coenzyme-A ligase-encoding gene (4CL216) from a hybrid poplar and the grapevine resveratrol synthase gene (vst1) in laboratory strains of S. cerevisiae. This yeast has the ability to metabolise p-coumaric acid, a substance already present in grape must. This compound was therefore added to the synthetic media used for the growth of laboratory cultures. Transformants expressing both the 4CL216 and vst1 genes were obtained and tested for production of resveratrol. Following beta-glucosidase treatment of organic extracts for removal of glucose moieties that are typically bound to resveratrol, the results showed that the yeast transformants had produced the resveratrol beta-glucoside, piceid. This is the first report of the reconstruction of a biochemical pathway in a heterologous host to produce resveratrol.     

Identification of pterostilbene as a phytoalexin from Vitis vinifera leaves

An inducible antifungal compound in grapevine leaves (Vitis vinifera L., cv Cabernet-Sauvignon) has been identified as trans-pterostilbene (3,5-dimethoxy-4′-hydroxy stilbene). It is only a minor component of the phytoalexin response of V. vinifera but its antifungal activity is relatively high by comparison with resveratrol and the viniferins, stress metabolites which have been identified previously in grapevine. Methods for the quantitative analysis of pterostilbene, resveratrol, ε- and α-viniferins by HPLC are described.     

<Emphasis Type="Italic">Escherichia coli</Emphasis> modular coculture system for resveratrol glucosides production

In bio-based fermentation, the overall bioprocess efficiency is significantly affected by the metabolic burden associated with the expression of complete biosynthetic pathway as well as precursor and cofactor generating enzymes into a single microbial cell. To attenuate such burden by compartmentalizing the enzyme expression, recently synthetic biologists have used coculture or poly-culture techniques for biomolecules synthesis. In this paper, coculture system of two metabolically engineered Escherichia coli populations were employed which comprises upstream module expressing two enzymes converting para-coumaric acid into resveratrol and the downstream module expressing glucosyltransferase to convert the resveratrol into its glucosidated forms; polydatin and resveratroloside. Upon optimization of the initial inoculum ratio of two E. coli populations, 92 mg resveratrol glucosides/L (236 µM) was produced i.e. achieving 84% bioconversion from 280 µM of p-coumaric acid in 60 h by 3 L fed batch fermentor. This is the report of applying coculture system to produce resveratrol glucosides by expressing the aglycone formation pathway and sugar dependent pathway into two different cells.     

Construction of a heat-inducible Escherichia coli strain for efficient de novo biosynthesis of l-tyrosine

l-Tyrosine is an important amino acid widely used in food, agriculture, and pharmaceutical industries. However, the industrial application was severely constrained due to low production. To obtain the Escherichia coli mutant producing l-tyrosine in abundance, the heat-inducible expression vector carrying the two feedback resistance enzymes (3-deoxy-7-phosphoheptulonate synthase encoded by aroG^fbr and chorismate mutase/prephenate dehydrogenase encoded by tyrA^fbr) were introduced into the phenylalanine-producing E. coli strain to enable it to synthesize l-tyrosine directly from glucose. Furthermore, the CRISPR-Cas9 technology was applied to eliminate l-phenylalanine and l-tryptophan pathways for their competition for the carbon flux. The global regulatory protein TyrR, which mediates the biosynthesis and transportation of aromatic amino acids, was also deleted to increase l-tyrosine production. Among the recombinant strains, the pheA/tyrR double-gene deletion strain had the highest yield of 5.84 g/L on shake flasks. The feeding strategies were then optimized in a 3-L fermentor. The pheA/tyrR double-gene deletion strain with the heat-inducible expression plasmid pAP-aroG^fbr-tyrA^fbr was able to produce 55.54 g/L l-tyrosine by fed-batch fermentation; the substrate conversion rate was 0.25 g/g. The recombinant strains constructed in this study could be an industrial platform for the microbial production of l-tyrosine directly from glucose.     

Action of ultraviolet-C on stilbene formation in callus ofArachis hypogaea

The action of light on the formation of stilbenes and the induction of stilbene synthase in dark-grown and light-grown callus of peanut (Arachis hypogaea) was investigated over the wavelength range from 250 to 400 nm. Ultraviolet light of 260–270 nm had a significant and selective effect on the formation of resveratrol and isopentenylresveratrol. The callus responded by the production of stilbene synthase, with maximal activity appearing 4 h after irradiation with a fluence rate of 1 W m^-2 (270 nm) applied for 10 min. At lower fluence rates, maximal responses in enzyme activity were shifted to longer induction periods. The efficiency of the biosynthetic pathway, and the form and maxima of enzyme profiles depended on the duration of exposure. We failed to demonstrate any significant influence of red light at low energy irradiation (672 nm, 726 nm and 753 nm).     

Metabolic Engineering for Resveratrol Derivative Biosynthesis in Escherichia coli

We previously reported that the SbROMT3syn recombinant protein catalyzes the production of the methylated resveratrol derivatives pinostilbene and pterostilbene by methylating substrate resveratrol in recombinant E. coli. To further study the production of stilbene compounds in E. coli by the expression of enzymes involved in stilbene biosynthesis, we isolated three stilbene synthase (STS) genes from rhubarb, peanut, and grape as well as two resveratrol O-methyltransferase (ROMT) genes from grape and sorghum. The ability of RpSTS to produce resveratrol in recombinant E. coli was compared with other AhSTS and VrSTS genes. Out of three STS, only AhSTS was able to produce resveratrol from p-coumaric acid. Thus, to improve the solubility of RpSTS, VrROMT, and SbROMT3 in E. coli, we synthesized the RpSTS, VrROMT and SbROMT3 genes following codon-optimization and expressed one or both genes together with the cinnamate/4-coumarate:coenzyme A ligase (CCL) gene from Streptomyces coelicolor. Our HPLC and LC-MS analyses showed that recombinant E. coli expressing both ScCCL and RpSTSsyn led to the production of resveratrol when p-coumaric acid was used as the precursor. In addition, incorporation of SbROMT3syn in recombinant E. coli cells produced resveratrol and its mono-methylated derivative, pinostilbene, as the major products from p-coumaric acid. However, very small amounts of pterostilbene were only detectable in the recombinant E. coli cells expressing the ScCCL, RpSTSsyn and SbROMT3syn genes. These results suggest that RpSTSsyn exhibits an enhanced enzyme activity to produce resveratrol and SbROMT3syn catalyzes the methylation of resveratrol to produce pinostilbene in E. coli cells.     

The origin of the nitrogen atom in the thiazole ring of thiamine in Escherichia coli

Methods are described for the isolation and gas chromatographic-mass spectrometric analysis of the 4-methyl-5-β-hydroxyethyl thiazole moiety of thiamine in microbial cells. Using these methods, it was determined that in Escherichia coli the nitrogen atom in the thiazole ring of thiamine is derived solely from l-tyrosine.     

Effect of plant stilbene precursors on the biosynthesis of resveratrol in Vitis amurensis Rupr. Cell cultures

The biosynthesis of resveratrol after the application of a precursor for biosynthesis, i.e., phenylalanine (Phe), has been studied. The application of Phe has been shown to increase significantly the expression of the phenylalanine-ammonia-lyase (PAL) and stilbene synthase (STS) genes and enhance the production of resveratrol by 8.5 times. Data on resveratrol production after the addition of Phe and coumaric acid (CA) were compared with known analogs.