Monooxygenase-catalyzed regioselective hydroxylation for the synthesis of hydroxyequols

Comparative analysis of substrate- and regio-selectivity of HpaB monooxygenases and their application to hydroxydaidzein synthesis

4-Hydroxyphenylacetate 3-hydroxylase (HpaB) has high potential for use in polyphenol synthesis via ortho-hydroxylation. Although the HpaB enzymes from Pseudomonas aeruginosa (PaHpaB) and Escherichia coli (EcHpaB) have been well studied, few studies have compared their activity and substrate selectivity. Thus, which HpaB is optimal for use in the biotechnological production of polyphenols is unclear. In this study, we performed a comparative analysis of the substrate- and regio-selectivity of PaHpaB, EcHpaB, and the recently discovered enzyme from Rhodococcus opacus (RoHpaB). The activity of these enzymes was first compared toward representative aromatic substrates. PaHpaB and EcHpaB exhibited very similar catalytic activity toward p-coumaric acid and tyrosol with one benzene ring, whereas PaHpaB exhibited greater activity than EcHpaB toward resveratrol and naringenin with two benzene rings. These results suggest that PaHpaB is superior to EcHpaB in converting bulky compounds. Furthermore, PaHpaB also exhibited catalytic activity toward a flavonoid, daidzein (7,4'-dihydroxyisoflavone), whereas EcHpaB did not. RoHpaB also exhibited strong activity toward daidzein in addition to other aromatic substrates. Interestingly, PaHpaB hydroxylated the 6-position of daidzein, whereas RoHpaB hydroxylated the 3'-position. PaHpaB and RoHpaB enabled the facile synthesis of not only 6-hydroxydaidzein and 3'-hydroxydaidzein but also 6,3'-dihydroxydaidzein via the cascade reaction. This study is the first to demonstrate synthesis of hydroxydaidzeins using HpaB enzymes.

Engineering a coenzyme-independent dioxygenase for one-step production of vanillin from ferulic acid

Vanillin is one of the world's most important flavor and fragrance compounds used in foods and cosmetics. In plants, vanillin is reportedly biosynthesized from ferulic acid via the hydratase/lyase-type enzyme VpVAN. However, in biotechnological and biocatalytic applications, the use of VpVAN limits the production of vanillin. Although microbial enzymes are helpful as substitutes for plant enzymes, synthesizing vanillin from ferulic acid in one step using microbial enzymes remains a challenge. Here, we developed a single enzyme that catalyzes vanillin production from ferulic acid in a coenzyme-independent manner via the rational design of a microbial dioxygenase in the carotenoid cleavage oxygenase family using computational simulations. This enzyme acquired catalytic activity toward ferulic acid by introducing mutations into the active center to increase its affinity for ferulic acid. We found that the single enzyme can catalyze not only the production of vanillin from ferulic acid but also the synthesis of other aldehydes from p-coumaric acid, sinapinic acid, and coniferyl alcohol. These results indicate that the approach used in this study can greatly expand the range of substrates available for the dioxygenase family of enzymes. The engineered enzyme enables efficient production of vanillin and other value-added aldehydes from renewable lignin-derived compounds.

IMPORTANCE

The final step of vanillin biosynthesis in plants is reportedly catalyzed by the enzyme VpVAN. Prior to our study, VpVAN was the only reported enzyme that directly converts ferulic acid to vanillin. However, as many characteristics of VpVAN remain unknown, this enzyme is not yet suitable for biocatalytic applications. We show that an enzyme that converts ferulic acid to vanillin in one step could be constructed by modifying a microbial dioxygenase-type enzyme. The engineered enzyme is of biotechnological importance as a tool for the production of vanillin and related compounds via biocatalytic processes and metabolic engineering. The results of this study may also provide useful insights for understanding vanillin biosynthesis in plants.

4-Hydroxyphenylacetate 3-Hydroxylase (4HPA3H): A Vigorous Monooxygenase for Versatile O-Hydroxylation Applications in the Biosynthesis of Phenolic Derivatives

4-Hydroxyphenylacetate 3-hydroxylase (4HPA3H) is a long-known class of two-component flavin-dependent monooxygenases from bacteria, including an oxygenase component (EC 1.14.14.9) and a reductase component (EC 1.5.1.36), with the latter being accountable for delivering the cofactor (reduced flavin) essential for o-hydroxylation. 4HPA3H has a broad substrate spectrum involved in key biological processes, including cellular catabolism, detoxification, and the biosynthesis of bioactive molecules. Additionally, it specifically hydroxylates the o-position of the C4 position of the benzene ring in phenolic compounds, generating high-value polyhydroxyphenols. As a non-P450 o-hydroxylase, 4HPA3H offers a viable alternative for the de novo synthesis of valuable natural products. The enzyme holds the potential to replace plant-derived P450s in the o-hydroxylation of plant polyphenols, addressing the current significant challenge in engineering specific microbial strains with P450s. This review summarizes the source distribution, structural properties, and mechanism of 4HPA3Hs and their application in the biosynthesis of natural products in recent years. The potential industrial applications and prospects of 4HPA3H biocatalysts are also presented.

Isolation and characterization of filamentous fungi capable of degrading the mycotoxin patulin

Patulin is a toxic secondary metabolite synthesized by various fungal strains. This mycotoxin is generally toxic to microorganisms as well as mammals due to its reactivity with the important cellular antioxidant glutathione. In this study, we explored the presence of microorganisms capable of degrading patulin. Microorganisms were screened for the ability to both grow in culture medium containing patulin and reduce its concentration. Screening of 510 soil samples resulted in the isolation of two filamentous fungal strains, one of which, Acremonium sp. TUS-MM1 was characterized in detail. Liquid chromatography-mass spectrometry and nuclear magnetic resonance analyses revealed that TUS-MM1 cells degraded patulin to desoxypatulinic acid. In addition, extracellular components of strain TUS-MM1 also exhibited patulin-transforming activity. High-performance liquid chromatography analysis revealed that the extracellular components generated several products from patulin. Disc diffusion assay using Escherichia coli cells revealed that the patulin-transformation products by the extracellular components are less toxic than patulin. We also demonstrated that a thermostable, low-molecular-weight compound within the extracellular components was responsible for the patulin-transforming activity. These results suggest that strain TUS-MM1 transforms patulin into less-toxic molecules by secreting a highly reactive compound. In addition, once patulin enters the cells, strain TUS-MM1 can transform it into desoxypatulinic acid to reduce its toxicity.

Discovery of diphenyl ether-degrading Streptomyces strains by direct screening based on ether bond-cleaving activity

Diphenyl ethers (DEs), which are widely used in the agricultural and chemical industries, have become hazardous contaminants in the environment. Although several DE-degrading bacteria have been reported, discovering new types of such microorganisms could enhance understanding of the degradation mechanism in the environment. In this study, we used a direct screening method based on detection of ether bond-cleaving activity to screen for microorganisms that degrade 4,4'-dihydroxydiphenyl ether (DHDE) as a model DE. Microorganisms isolated from soil samples were incubated with DHDE, and strains producing hydroquinone via ether bond cleavage were selected using hydroquinone-sensitive Rhodanine reagent. This screening procedure resulted in the isolation of 3 bacteria and 2 fungi that transform DHDE. Interestingly, all of the isolated bacteria belonged to one genus, Streptomyces. To our knowledge, these are the first microorganisms of the genus Streptomyces shown to degrade a DE. Streptomyces sp. TUS-ST3 exhibited high and stable DHDE-degrading activity. HPLC, LC-MS, and GC-MS analyses revealed that strain TUS-ST3 converts DHDE to its hydroxylated analogue and generates hydroquinone as an ether bond-cleavage product. Strain TUS-ST3 also transformed DEs other than DHDE. In addition, glucose-grown TUS-ST3 cells began to transform DHDE after incubation with this compound for 12 h, and produced 75 μM hydroquinone in 72 h. These activities of streptomycetes may play an important role in DE degradation in the environment. We also report the whole genome sequence of strain TUS-ST3.

Engineering a Prokaryotic Non-P450 Hydroxylase for 3'-Hydroxylation of Flavonoids

Plant-derived cytochrome P450-dependent flavonoid 3'-hydroxylases are the rate-limiting enzymes in flavonoid biosynthesis. In this study, the large component (HpaB) of a prokaryotic 4-hydroxyphenylacetate (4-HPA) 3-hydroxylase was engineered for efficient 3'-hydroxylation of naringenin. First, we selected four HpaBs through database search and phylogenetic analysis and compared their catalytic activities toward 4-HPA and naringenin. HpaB from Rhodococcus opacus B-4 (RoHpaB) showed better preference toward naringenin. To elucidate the underlying mechanism, we analyzed the structural differences of HpaBs through homologous modeling, molecular docking, and molecular dynamics simulation, and the substrate preference of RoHpaB was mainly attributed to the shorter chain length of loop 212-222 and the larger substrate binding pocket. RoHpaB was further engineered by alanine scanning and structural replacement, and the RoHpaB^Y215A variant was obtained, whose catalytic efficiency (k_cat/K_m) toward naringenin is 25.3 times higher than that of RoHpaB. In addition, RoHpaB^Y215A also showed significantly improved activity toward flavonoids apigenin and kaempferol. This work opens the possibility of using engineered HpaB as a versatile hydroxylase to produce functionalized flavonoids.

Biocatalytic synthesis and evaluation of antioxidant and antibacterial activities of hydroxyequols

Hydroxyequols are promising analogues of the biologically active flavonoid, equol. We recently found that the flavin-dependent monooxygenase HpaB_ro-3 of Rhodococcus opacus regioselectively synthesizes 3'-hydroxyequol from equol, whereas HpaB_pl-1 of Photorhabdus luminescens synthesizes 6-hydroxyequol. In this study, we investigated the cascade synthesis of a dihydroxyequol compound from equol using these two enzymes. When Escherichia coli cells expressing HpaB_ro-3 and cells expressing HpaB_pl-1 were simultaneously incubated with equol, the cells efficiently synthesized 6,3'-dihydroxyequol (8.7 mM, 2.4 g/L) via 3'- and 6-hydroxyequols in one pot. The antioxidant activity of the equol derivatives increased with an increase in the number of hydroxyl groups on the equol scaffold. 6,3'-Dihydroxyequol exhibited potent antioxidant activity. In addition, 6-hydroxyequol significantly inhibited the growth of E. coli. Cell survival studies suggested that 6-hydroxyequol is a bactericidal rather than bacteriostatic compound. To our knowledge, this is the first report describing the antibacterial activity of hydroxyequols.

Oxygenating Biocatalysts for Hydroxyl Functionalisation in Drug Discovery and Development

C-H oxyfunctionalisation remains a distinct challenge for synthetic organic chemists. Oxygenases and peroxygenases (grouped here as "oxygenating biocatalysts") catalyse the oxidation of a substrate with molecular oxygen or hydrogen peroxide as oxidant. The application of oxygenating biocatalysts in organic synthesis has dramatically increased over the last decade, producing complex compounds with potential uses in the pharmaceutical industry. This review will focus on hydroxyl functionalisation using oxygenating biocatalysts as a tool for drug discovery and development. Established oxygenating biocatalysts, such as cytochrome P450s and flavin-dependent monooxygenases, have widely been adopted for this purpose, but can suffer from low activity, instability or limited substrate scope. Therefore, emerging oxygenating biocatalysts which offer an alternative will also be covered, as well as considering the ways in which these hydroxylation biotransformations can be applied in drug discovery and development, such as late-stage functionalisation (LSF) and in biocatalytic cascades.

Sustainable Approach for Peroxygenase-Catalyzed Oxidation Reactions Using Hydrogen Peroxide Generated from Spent Coffee Grounds and Tea Leaf Residues

Peroxygenases are promising catalysts for use in the oxidation of chemicals as they catalyze the direct oxidation of a variety of compounds under ambient conditions using hydrogen peroxide (H₂O₂) as an oxidant. Although the use of peroxygenases provides a simple method for oxidation of chemicals, the anthraquinone process currently used to produce H₂O₂ requires significant energy input and generates considerable waste, which negatively affects process sustainability and production costs. Thus, generating H₂O₂ for peroxygenases on site using an environmentally benign method would be advantageous. Here, we utilized spent coffee grounds (SCGs) and tea leaf residues (TLRs) for the production of H₂O₂. These waste biomass products reacted with molecular oxygen and effectively generated H₂O₂ in sodium phosphate buffer. The resulting H₂O₂ was utilized by the bacterial P450 peroxygenase, CYP152A1. Both SCG-derived and TLR-derived H₂O₂ promoted the CYP152A1-catalyzed oxidation of 4-methoxy-1-naphthol to Russig's blue as a model reaction. In addition, when CYP152A1 was incubated with styrene, the SCG and TLR solutions enabled the synthesis of styrene oxide and phenylacetaldehyde. This new approach using waste biomass provides a simple, cost-effective, and sustainable oxidation method that should be readily applicable to other peroxygenases for the synthesis of a variety of valuable chemicals.

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.

Isolation and characterization of microorganisms capable of cleaving the ether bond of 2-phenoxyacetophenone

Lignin is a heterogeneous aromatic polymer and major component of plant cell walls. The β-O-4 alkyl aryl ether is the most abundant linkage within lignin. Given that lignin is effectively degraded on earth, as yet unknown ether bond-cleaving microorganisms could still exist in nature. In this study, we searched for microorganisms that transform 2-phenoxyacetophenone (2-PAP), a model compound for the β-O-4 linkage in lignin, by monitoring ether bond cleavage. We first isolated microorganisms that grew on medium including humic acid (soil-derived organic compound) as a carbon source. The isolated microorganisms were subsequently subjected to colorimetric assay for 2-PAP ether bond-cleaving activity; cells of the isolated strains were incubated with 2-PAP, and strains producing phenol via ether bond cleavage were selected using phenol-sensitive Gibbs reagent. This screening procedure enabled the isolation of various 2-PAP-transforming microorganisms, including 7 bacteria (genera: Acinetobacter, Cupriavidus, Nocardioides, or Streptomyces) and 1 fungus (genus: Penicillium). To our knowledge, these are the first microorganisms demonstrated to cleave the ether bond of 2-PAP. One Gram-negative bacterium, Acinetobacter sp. TUS-SO1, was characterized in detail. HPLC and GC-MS analyses revealed that strain TUS-SO1 oxidatively and selectively cleaves the ether bond of 2-PAP to produce phenol and benzoate. These results indicate that the transformation mechanism differs from that involved in reductive β-etherase, which has been well studied. Furthermore, strain TUS-SO1 efficiently transformed 2-PAP; glucose-grown TUS-SO1 cells converted 1 mM 2-PAP within only 12 h. These microorganisms might play important roles in the degradation of lignin-related compounds in nature.

Diversity and characteristics of culturable endophytic bacteria from Passiflora edulis seeds

Defense compounds generally inhibit microbial colonization of plants. In this study, we examined the presence of endophytes in Passiflora edulis seeds that accumulate resveratrol and piceatannol at extremely high levels as defense compounds. Interestingly, although no microbial colonies appeared on an agar growth medium from the cut or homogenized seeds, colonies were generated from cut seedlings derived from the seeds. A total of 19 bacterial strains were isolated, of which 15 were classified as Gram-positive. As we hypothesized that extremely high levels of piceatannol in the seeds would inhibit the growth of endophytes cultured directly from the seeds, we examined the antimicrobial activity of this compound against the isolated bacteria. Piceatannol exerted bacteriostatic rather than bactericidal effects on most of the bacteria tested. These results suggest that the bacteria remain static in the seeds due to the presence of piceatannol and are transmitted to the seedlings during the germination process, enabling colonies to be established from the seedlings on the agar medium. We also investigated the biocatalytic activity of the isolated bacteria toward resveratrol and piceatannol. One bacterium, Brevibacterium sp. PE28-2, converted resveratrol and piceatannol to their respective derivatives. This strain is the first endophyte shown to exhibit such activity.

Flavoprotein monooxygenases: Versatile biocatalysts

Flavoprotein monooxygenases (FPMOs) are single- or two-component enzymes that catalyze a diverse set of chemo-, regio- and enantioselective oxyfunctionalization reactions. In this review, we describe how FPMOs have evolved from model enzymes in mechanistic flavoprotein research to biotechnologically relevant catalysts that can be applied for the sustainable production of valuable chemicals. After a historical account of the development of the FPMO field, we explain the FPMO classification system, which is primarily based on protein structural properties and electron donor specificities. We then summarize the most appealing reactions catalyzed by each group with a focus on the different types of oxygenation chemistries. Wherever relevant, we report engineering strategies that have been used to improve the robustness and applicability of FPMOs.