Production of bioactive hydroxyflavones by using monooxygenase from Saccharothrix espanaensis

Soy Extract, Rich in Hydroxylated Isoflavones, Exhibits Antidiabetic Properties In Vitro and in Drosophila melanogaster In Vivo

In the context of the growing prevalence of type 2 diabetes (T2DM), control of postprandial hyperglycemia is crucial for its prevention. Blood glucose levels are determined by various factors including carbohydrate hydrolyzing enzymes, the incretin system and glucose transporters. Furthermore, inflammatory markers are recognized predictors of diabetes outcome. Although there is some evidence that isoflavones may exhibit anti-diabetic properties, little is known about to what extent their corresponding hydroxylated metabolites may affect glucose metabolism. We evaluated the ability of a soy extract before (pre-) and after (post-) fermentation to counteract hyperglycemia in vitro and in Drosophila melanogaster in vivo. Fermentation with Aspergillus sp. JCM22299 led to an enrichment of hydroxy-isoflavones (HI), including 8-hydroxygenistein, 8-hydroxyglycitein and 8-hydroxydaidzein, accompanied by an enhanced free radical scavenging activity. This HI-rich extract demonstrated inhibitory activity towards α-glucosidase and a reduction of dipeptidyl peptidase-4 enzyme activity. Both the pre- and post-fermented extracts significantly inhibited the glucose transport via sodium-dependent glucose transporter 1. Furthermore, the soy extracts reduced c-reactive protein mRNA and secreted protein levels in interleukin-stimulated Hep B3 cells. Finally, supplementation of a high-starch D. melanogaster diet with post-fermented HI-rich extract decreased the triacylglyceride content of female fruit flies, confirming its anti-diabetic properties in an in vivo model.

Crystal Structure and Biochemical Analysis of a Cytochrome P450 CYP101D5 from Sphingomonas echinoides

Cytochrome P450 enzymes (CYPs) are heme-containing enzymes that catalyze hydroxylation with a variety of biological molecules. Despite their diverse activity and substrates, the structures of CYPs are limited to a tertiary structure that is similar across all the enzymes. It has been presumed that CYPs overcome substrate selectivity with highly flexible loops and divergent sequences around the substrate entrance region. Here, we report the newly identified CYP101D5 from Sphingomonas echinoides. CYP101D5 catalyzes the hydroxylation of β-ionone and flavonoids, including naringenin and apigenin, and causes the dehydrogenation of α-ionone. A structural investigation and comparison with other CYP101 families indicated that spatial constraints at the substrate-recognition site originate from the B/C loop. Furthermore, charge distribution at the substrate binding site may be important for substrate selectivity and the preference for CYP101D5.

Engineering of Microbial Substrate Promiscuous CYP105A5 for Improving the Flavonoid Hydroxylation

Bacterial cytochrome P450 (CYP) enzymes are versatile biocatalysts that are responsible for the biotransformation of diverse endogenous substances. CYP105A5 from Streptomyces sp. showed substrate flexibility with different flavonoids and was able to catalyze O-demethylation of biochanin A, regioselective C3′-hydroxylation of daidzein, genistein, and naringenin, and additional C8-hydroxylation for daidzein using heterologous redox partners putidaredoxin and putidaredoxin reductase. By rational design of substrate-binding pocket based on experimental data, homology modeling, and molecular docking analysis, we enhanced the product formation rate of flavonoids. The double mutant L100A/I302A and L100A/I408N exhibited greatly enhanced in vivo conversion rates for flavonoid hydroxylation. Particularly, the L100A/I302A mutant’s kcat/Km values and in vivo conversion rate increased by 1.68-fold and 2.57-fold, respectively, for naringenin. Overall, our result might facilitate the potential use of CYP105A5 for future modification and application in whole-cell biocatalysts for the production of valuable polyphenols.

Novel flavonoid C-8 hydroxylase from Rhodotorula glutinis: identification, characterization and substrate scope

Background

The regioselective hydroxylation of phenolic compounds, especially flavonoids, is still a bottleneck of classical organic chemistry that could be solved using enzymes with high activity and specificity. Yeast Rhodotorula glutinis KCh735 in known to catalyze the C-8 hydroxylation of flavones and flavanones. The enzyme F8H (flavonoid C8-hydroxylase) is involved in the reaction, but the specific gene has not yet been identified. In this work, we present identification, heterologous expression and characterization of the first F8H ortho-hydroxylase from yeast.

Results

Differential transcriptome analysis and homology to bacterial monooxygenases, including also a FAD-dependent motif and a GD motif characteristic for flavin-dependent monooxygenases, provided a set of coding sequences among which RgF8H was identified. Phylogenetic analysis suggests that RgF8H is a member of the flavin monooxygenase group active on flavonoid substrates. Analysis of recombinant protein showed that the enzyme catalyzes the C8-hydroxylation of naringenin, hesperetin, eriodyctiol, pinocembrin, apigenin, luteolin, chrysin, diosmetin and 7,4ʹ-dihydroxyflavone. The presence of the C7-OH group is necessary for enzymatic activity indicating ortho-hydroxylation mechanism. The enzyme requires the NADPH coenzyme for regeneration prosthetic group, displays very low hydroxyperoxyflavin decupling rate, and addition of FAD significantly increases its activity.

Conclusions

This study presents identification of the first yeast hydroxylase responsible for regioselective C8-hydroxylation of flavonoids (F8H). The enzyme was biochemically characterized and applied in in vitro cascade with Bacillus megaterium glucose dehydrogenase reactions. High in vivo activity in Escherichia coli enable further synthetic biology application towards production of rare highly antioxidant compounds.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01899-x.

Modification of flavonoids: methods and influences on biological activities

Flavonoids are important active ingredients in plant-based food, which have many beneficial effects on health. But the low solubility, poor oral bioavailability, and inferior stability of many flavonoids may limit their applications in the food, cosmetics, and pharmaceutical industries. Structural modification can overcome these shortcomings to improve and extend the application of flavonoids. The study of how to modify flavonoids and the influence of various modifications on biological activity have drawn great interest in the current literature. In this review, the working principles and operating conditions of modification methods were summarized along with their potential and limitations in terms of operational safety, cost, and productivity. The influence of various modifications on biological activities and the structure-activity relationships of flavonoids derivatives were discussed and highlighted, which may give guidance for the synthesis of highly effective active agents. In addition, the safety of flavonoids derivatives is reviewed, and future research directions of flavonoid modification research are discussed.

Regioselective One-Pot Synthesis of Hydroxy-(S)-Equols Using Isoflavonoid Reductases and Monooxygenases and Evaluation of the Hydroxyequol Derivatives as Selective Estrogen Receptor Modulators and Antioxidants

Several regiospecific enantiomers of hydroxy-(S)-equol (HE) were enzymatically synthesized from daidzein and genistein using consecutive reduction (four daidzein-to-equol–converting reductases) and oxidation (4-hydroxyphenylacetate 3-monooxygenase, HpaBC). Despite the natural occurrence of several HEs, most of them had not been studied owing to the lack of their preparation methods. Herein, the one-pot synthesis pathway of 6-hydroxyequol (6HE) was developed using HpaBC (EcHpaB) from Escherichia coli and (S)-equol-producing E. coli, previously developed by our group. Based on docking analysis of the substrate or products, a potential active site and several key residues for substrate binding were predicted to interpret the (S)-equol hydroxylation regioselectivity of EcHpaB. Through investigating mutations on the key residues, the T292A variant was verified to display specific mono-ortho-hydroxylation activity at C6 without further 3′-hydroxylation. In the consecutive oxidoreductive bioconversion using T292A, 0.95 mM 6HE could be synthesized from 1 mM daidzein, while 5HE and 3′HE were also prepared from genistein and 3′-hydroxydaidzein (3′HD or 3′-ODI), respectively. In the following efficacy tests, 3′HE and 6HE showed about 30∼200-fold higher EC50 than (S)-equol in both ERα and ERβ, and they did not have significant SERM efficacy except 6HE showing 10% lower β/α ratio response than that of 17β-estradiol. In DPPH radical scavenging assay, 3′HE showed the highest antioxidative activity among the examined isoflavone derivatives: more than 40% higher than the well-known 3′HD. In conclusion, we demonstrated that HEs could be produced efficiently and regioselectively through the one-pot bioconversion platform and evaluated estrogenic and antioxidative activities of each HE regio-isomer for the first time.

Evolution-aided engineering of plant specialized metabolism

The evolution of new traits in living organisms occurs via the processes of mutation, recombination, genetic drift, and selection. These processes that have resulted in the immense biological diversity on our planet are also being employed in metabolic engineering to optimize enzymes and pathways, create new-to-nature reactions, and synthesize complex natural products in heterologous systems. In this review, we discuss two evolution-aided strategies for metabolic engineering-directed evolution, which improves upon existing genetic templates using the evolutionary process, and combinatorial pathway reconstruction, which brings together genes evolved in different organisms into a single heterologous host. We discuss the general principles of these strategies, describe the technologies involved and the molecular traits they influence, provide examples of their use, and discuss the roadblocks that need to be addressed for their wider adoption. A better understanding of these strategies can provide an impetus to research on gene function discovery and biochemical evolution, which is foundational for improved metabolic engineering. These evolution-aided approaches thus have a substantial potential for improving our understanding of plant metabolism in general, for enhancing the production of plant metabolites, and in sustainable agriculture.

Recent Advances in Heterologous Synthesis Paving Way for Future Green-Modular Bioindustries: A Review With Special Reference to Isoflavonoids

Isoflavonoids are well-known plant secondary metabolites that have gained importance in recent time due to their multiple nutraceutical and pharmaceutical applications. In plants, isoflavonoids play a role in plant defense and can confer the host plant a competitive advantage to survive and flourish under environmental challenges. In animals, isoflavonoids have been found to interact with multiple signaling pathways and have demonstrated estrogenic, antioxidant and anti-oncologic activities in vivo. The activity of isoflavonoids in the estrogen pathways is such that the class has also been collectively called phytoestrogens. Over 2,400 isoflavonoids, predominantly from legumes, have been identified so far. The biosynthetic pathways of several key isoflavonoids have been established, and the genes and regulatory components involved in the biosynthesis have been characterized. The biosynthesis and accumulation of isoflavonoids in plants are regulated by multiple complex environmental and genetic factors and interactions. Due to this complexity of secondary metabolism regulation, the export and engineering of isoflavonoid biosynthetic pathways into non-endogenous plants are difficult, and instead, the microorganisms Saccharomyces cerevisiae and Escherichia coli have been adapted and engineered for heterologous isoflavonoid synthesis. However, the current ex-planta production approaches have been limited due to slow enzyme kinetics and traditionally laborious genetic engineering methods and require further optimization and development to address the required titers, reaction rates and yield for commercial application. With recent progress in metabolic engineering and the availability of advanced synthetic biology tools, it is envisaged that highly efficient heterologous hosts will soon be engineered to fulfill the growing market demand.

Altering the Regioselectivity of Cytochrome P450 BM3 Variant M13 toward Genistein through Protein Engineering and Variation of Reaction Conditions

The biocatalysts responsible for the enzymatic synthesis of hydroxygenisteins, derivatives of genistein with multiple activities, usually show regioselective promiscuity, hydroxylating genistein to form a mixture of multiple products, which, in turn, results in a cumbersome separation and purification. Hence, it is highly desired to explore the underlying mechanism regulating the regioselectivity of hydroxylases. M13 is a variant of cytochrome P450 BM3 with oxidant activity toward genistein. Herein, genistein was demonstrated to be hydroxylated by M13 to form a mixture of 3'-hydroxygenistein (3'-OHG) and 8-hydroxygenistein (8-OHG), each giving 4% conversion with a ratio of 1:1. Protein engineering toward M13 was thus performed to improve its regioselectivity. When isoleucine at position 86 was mutated into cysteine, the resultant variant M13I86C displayed improved regioselectivity toward 3'-OHG with an increased conversion of 8.5%. The double mutation M13I86CP18W further boosted the conversion of 3'-OHG to 9.6%, and the ratio of 3'-OHG to 8-OHG increased to 12:1. Conversely, both CoCl₂ and glucose 6-phosphate (G6P) could lead to more 8-OHG. When Co²⁺ reached 37.5 mM, M13I86CP18W could give an 8-OHG conversion of 22.4%. The maximal ratio of 8-OHG to 3'-OHG reached 130 when 62.5 mM Co²⁺ was included in the reaction mixture. With the increase of G6P from 10 to 40 mM, the conversion of M13I86CP18W to 8-OHG gradually increased to 22.6%, while the conversion to 3'-OHG decreased to 6%. Thus, both intrinsic residues and external reaction conditions can affect the regiospecificity of M13, which laid the foundation for the selection of suitable biocatalysts for the hydroxylation of genistein.

A new isoflavone glycoside from flowers of Pueraria Montana var. lobata (Willd.) Sanjappa & Pradeep

A new isoflavone glycoside, named 3'-hydroxytectorigenin-7-O-β-D-xylosyl-(1→6)-β-D-glucopyranoside (1) was isolated from the flowers of Pueraria montana var. lobata (Willd.) Sanjappa & Pradeep. The structure of compound 1 was characterised by HR-ESI-MS and NMR spectroscopic methods. In radical scavenging activity test using 2, 2-diphenyl-1-picrylhydrazyl (DPPH), compound 1 showed moderate activity with IC₅₀ value of 42 ± 4.2 μg/mL.

Recent advances in the microbial hydroxylation and reduction of soy isoflavones

Soy isoflavones are naturally occurring phytochemicals, which are biotransformed into functional derivatives through oxidative and reductive metabolic pathways of diverse microorganisms. Such representative derivatives, ortho-dihydroxyisoflavones (ODIs) and equols, have attracted great attention for their versatile health benefits since they were found from soybean fermented foods and human intestinal fluids. Recently, scientists in food technology, nutrition and microbiology began to understand their correct biosynthetic pathways and nutraceutical values, and have attempted to produce the valuable bioactive compounds using microbial fermentation and whole-cell/enzyme-based biotransformation. Furthermore, artificial design of microbial catalysts and/or protein engineering of oxidoreductases were also conducted to enhance production efficiency and regioselectivity of products. This minireview summarizes and introduces the past year's studies and recent advances in notable production of ODIs and equols, and provides information on available microbial species and their catalytic performance with perspectives on industrial application.

Antimicrobial and Cytotoxic Properties of Bioactive Metabolites Produced by Streptomyces cavourensis YBQ59 Isolated from Cinnamomum cassia Prels in Yen Bai Province of Vietnam

The endophytic actinomycete strain YBQ59 was isolated from Cinnamomum cassia Prels in Yen Bai province (21°53'14″N; 104°35'9″E) of northern Vietnam. Based on analysis of morphological, physiological characteristics and 16S rRNA gene sequence (GenBank Acc. No. MF950891), the strain YBQ59 possessed high similarity to Streptomyces cavourensis subsp. cavourensis strain NRRL 2740, therefore assigned as S. cavourensis YBQ59. The ethyl acetate extract of the YBQ59 culture broth isolated eight pure secondary metabolites, identified as 1-monolinolein (1), bafilomycin D (2), nonactic acid (3), daidzein (4), 3'-hydroxydaidzein (5), 5,11-epoxy-10-cadinanol (6), prelactone B (7), and daucosterol (8). Compounds 1, 3-8 were reported for the first time from S. cavourensis. Compounds 1-5 exhibited antimicrobial activities against both methicillin-resistant Staphylococcus aureus ATCC 33591 (MRSA) and methicillin-resistant Staphylococcus epidermidis ATCC 35984 (MRSE) among which the compound 1 revealed the strongest effects with minimum inhibitory concentrations of 8.5 and 14.6 µg/mL, respectively. The compound 2 showed high potential effect against MRSA (MIC of 11.1 µg/mL) but less effect against MRSE (MIC of 30.3 µg/mL). The cytotoxicity of the compounds 1-7 was investigated against human lung adenocarcinoma EGFR-TKI-resistant cells, among which compounds 1, 2, and 5 exhibited the strong effect against A549 cells with IC₅₀ values of 3.6, 6.7, and 7.8 µM, respectively. Taken together, the experimental findings in this study suggested that the compounds 1 and 2 could be reproducible metabolites applicable for inhibition of both drug-resistant bacteria and cancer cell lines.

Production of three phenylethanoids, tyrosol, hydroxytyrosol, and salidroside, using plant genes expressing in Escherichia coli

Polyphenols, which include phenolic acids, flavonoids, stilbenes, and phenylethanoids, are generally known as useful antioxidants. Tyrosol, hydroxytyrosol, and salidroside are typical phenylethanoids. Phenylethanoids are found in plants such as olive, green tea, and Rhodiola and have various biological activities, including the prevention of cardiovascular diseases, cancer, and brain damage. We used Escherichia coli to synthesize three phenylethanoids, tyrosol, hydroxytyrosol, and salidroside. To synthesize tyrosol, the aromatic aldehyde synthase (AAS) was expressed in E. coli. Hydroxytyrosol was synthesized using E. coli harboring AAS and HpaBC, which encodes hydroxylase. In order to synthesize salidroside, 12 uridine diphosphate-dependent glycosyltransferases (UGTs) were screened and UGT85A1 was found to convert tyrosol to salidroside. Using E. coli harboring AAS and UGT85A1, salidroside was synthesized. Through the optimization of these three E. coli strains, we were able to synthesize 531 mg/L tyrosol, 208 mg/L hydroxytyrosol, and 288 mg/L salidroside, respectively.

Improving Free Radical Scavenging Activity of Soy Isoflavone Glycosides Daidzin and Genistin by 3'-Hydroxylation Using Recombinant Escherichia coli

The present study describes the biotransformation of a commercially available crude extract of soy isoflavones, which contained significant amounts of the soy isoflavone glycosides daidzin and genistin, by recombinant Escherichia coli expressing tyrosinase from Bacillus megaterium. Two major products were isolated from the biotransformation and identified as 3'-hydroxydaidzin and 3'-hydroxygenistin, respectively, based on their mass and nuclear magnetic resonance spectral data. The two 3'-hydroxyisoflavone glycosides showed potent 2,2-diphenyl-1-picrylhydrazyl free radical scavenging activity with IC50 values of 7.4 and 9.8 μM for 3'-hydroxydaidzin and 3'-hydroxygenistin, respectively. The free radical scavenging activities of the two 3'-hydroxyisoflavone glycosides were, respectively, 120 and 72 times higher than the activity of their precursors, daidzin and genistin, and were also stronger than the activity of ascorbic acid, which showed an IC50 value of 15.1 μM. This is the first report of the bio-production and potential antioxidant applications of both 3'-hydroxydaidzin and 3'-hydroxygenistin.

When plants produce not enough or at all: metabolic engineering of flavonoids in microbial hosts

As a result of the discovery that flavonoids are directly or indirectly connected to health, flavonoid metabolism and its fascinating molecules that are natural products in plants, have attracted the attention of both the industry and researchers involved in plant science, nutrition, bio/chemistry, chemical bioengineering, pharmacy, medicine, etc. Subsequently, in the past few years, flavonoids became a top story in the pharmaceutical industry, which is continually seeking novel ways to produce safe and efficient drugs. Microbial cell cultures can act as workhorse bio-factories by offering their metabolic machinery for the purpose of optimizing the conditions and increasing the productivity of a selective flavonoid. Furthermore, metabolic engineering methodology is used to reinforce what nature does best by correcting the inadequacies and dead-ends of a metabolic pathway. Combinatorial biosynthesis techniques led to the discovery of novel ways of producing natural and even unnatural plant flavonoids, while, in addition, metabolic engineering provided the industry with the opportunity to invest in synthetic biology in order to overcome the currently existing restricted diversification and productivity issues in synthetic chemistry protocols. In this review, is presented an update on the rationalized approaches to the production of natural or unnatural flavonoids through biotechnology, analyzing the significance of combinatorial biosynthesis of agricultural/pharmaceutical compounds produced in heterologous organisms. Also mentioned are strategies and achievements that have so far thrived in the area of synthetic biology, with an emphasis on metabolic engineering targeting the cellular optimization of microorganisms and plants that produce flavonoids, while stressing the advances in flux dynamic control and optimization. Finally, the involvement of the rapidly increasing numbers of assembled genomes that contribute to the gene- or pathway-mining in order to identify the gene(s) responsible for producing species-specific secondary metabolites is also considered herein.

Isolation, bioactivity, and production of ortho-hydroxydaidzein and ortho-hydroxygenistein

Daidzein and genistein are two major components of soy isoflavones. They exist abundantly in plants and possess multiple bioactivities. In contrast, ortho-hydroxydaidzein (OHD) and ortho-hydroxygenistein (OHG), including 6-hydroxydaidzein (6-OHD), 8-hydroxydaidzein (8-OHD), 3'-hydroxydaidzein (3'-OHD), 6-hydroxygenistein (6-OHG), 8-hydroxygenistein (8-OHG), and 3'-hydroxygenistein (3'-OHG), are rarely found in plants. Instead, they are usually isolated from fermented soybean foods or microbial fermentation broth feeding with soybean meal. Accordingly, the bioactivity of OHD and OHG has been investigated less compared to that of soy isoflavones. Recently, OHD and OHG were produced by genetically engineering microorganisms through gene cloning of cytochrome P450 (CYP) enzyme systems. This success opens up bioactivity investigation and industrial applications of OHD and OHG in the future. This article reviews isolation of OHD and OHG from non-synthetic sources and production of the compounds by genetically modified microorganisms. Several bioactivities, such as anticancer and antimelanogenesis-related activities, of OHD and OHG, are also discussed.