Properties and Mechanisms of Flavin-Dependent Monooxygenases and Their Applications in Natural Product Synthesis

Mechanistic and molecular insights into iterative triepoxidation catalyzed by monooxygenase MonCI using a natural substrate analog

Monensin, a polyether antibiotic produced by Streptomyces cinnamonensis, is synthesized through a series of stereospecific epoxidations orchestrated by the FAD-dependent monooxygenase MonCI. This study presents the crystal structure of MonCI in complex with a substrate analog, farnesyl acetate, which undergoes in vitro epoxidation at all three olefinic sites by MonCI. Additionally, we have solved the crystal structures of MonCI in complex with mono- and bis-epoxide intermediates. Structural analysis revealed that the interactions between MonCI and its substrate are predominantly hydrophobic, with residue Y208 playing a crucial role in substrate translocation. Computational modeling emphasizes the importance of FAD proximity to each olefinic group for efficient catalysis, providing insight into the mechanistic pathways for the first, second, and third epoxidations. Notably, when combined with electrochemical techniques, the yield of tri-epoxide farnesyl acetate reached 94 %, surpassing traditional enzymatic catalysis. This work not only elucidates the catalytic mechanism of MonCI but also underscores its potential as an effective biocatalyst for processive epoxidation in organic synthesis.

RNA interference-mediated targeting of monooxygenase SsMNO1 for controlling Sclerotinia stem rot caused by Sclerotinia sclerotiorum

BACKGROUND

Sclerotinia sclerotiorum is a devastating fungal pathogen that poses a threat to a variety of economically important crops. Owing to the lack of highly resistant cultivars and the prolonged survival of sclerotia, effective control of Sclerotinia diseases remains challenging. RNA interference (RNAi) agents targeting essential active transcripts of genes associated with the development and virulence of pathogens are a valuable and promising disease control method.

RESULTS

Our finding suggested that a flavin adenine dinucleotide (FAD)-dependent monooxygenase gene SsMNO1 plays pivotal roles in the hyphal growth, sclerotial development, and virulence of S. sclerotiorum, rendering it a potential target for RNAi-mediated management of S. sclerotiorum. The external application of double-stranded RNA (dsRNA) targeting SsMNO1 inhibited sclerotial development in artificial media and plant tissues. Furthermore, dsRNA significantly reduced the hyphal virulence of S. sclerotiorum in host plants by interfering with SsMNO1 expression. The inhibitory activity persisted for over 1 week on the surface of Brassica napus. Artificial small interfering RNA (siRNA) targeting SsMNO1 also exhibited inhibitory effects. Transgenic Arabidopsis thaliana plants expressing SsMNO1 hairpin RNAi constructs showed increased resistance to S. sclerotiorum infection. Notably, the total RNA extracts from SsMNO1-RNAi plants also reduced the hyphal virulence in Brassica napus.

CONCLUSIONS

Therefore, RNAi agents targeting SsMNO1 have dual effects on sclerotial development and hyphal virulence, rendering it an ideal target for controlling diseases caused by S. sclerotiorum. © 2024 Society of Chemical Industry.

Construction of Escherichia coli Cell Factory for Efficient Synthesis of Indigo

Indigo is widely used in dyes, medicines and semiconductors materials due to its excellent dyeing efficiency, antibacterial, antiviral, anticancer, anti-corrosion, and thermostability properties. Here, a biosynthetic pathway for indigo was designed, integrating two enzymes (EcTnaA, MaFMO) into a higher L-tryptophan-producing the strain Escherichia coli TRP. However, the lower catalytic activity of MaFMO was a bottleneck for increasing indigo titers. To overcome this limitation, the enzyme activity of MaFMO was enhanced through mechanism-guided rational design. The optimal mutant obtained in this study, MaFMOD197E, whose kcat/Km was 1.34 times that of the wild type, and its specific activity was 2.36 times that of the wild type. In addition, the expression levels of EcTnaA and MaFMOD197E were regulated by optimizing the promoters and increasing the copy number to generate the strain E. coli IND-13. Finally, in the optimal fermentation conditions (220 rpm, 0.05 % Tween-80), the strain E. coli IND-13 achieved the indigo titer of 568.52 mg/L in a 5-L bioreactor, with the yield and productivity of 2.62 mg/g and 12.96 mg/L/h (the highest to date), respectively. The results presented here can lay a foundation for further construction of cell factories for indigo and its derivatives with industrial application potential.

Mechanistic Perspective on Oxygen Activation Chemistry by Flavoenzymes

Flavin-dependent enzymes catalyze a panoply of chemical transformations essential for living organisms. Through oxygen activation, flavoenzymes could generate diverse flavin-oxygen species that mediate numerous redox and non-redox transformations. In this review, we highlight the extensive oxygen activation chemistry at two sites of the flavin cofactor: C4a and N5 sites. Oxygen activation at the C4a site generates flavin-C4aOO(H) species for various monooxygenation reactions, while activation at the N5 site produces negatively charged flavin-N5OOH species, which act as highly reactive nucleophiles or bases. The selective oxygen activation at either the C4a or N5 site depends on the nature of substrates and is controlled by the active site architecture. These insights have expanded our understanding of oxygen activation chemistry in flavoenzymes and will serve as a foundation for future efforts in enzyme engineering and redesign.

Unraveling proton-coupled electron transfer in cofactor-free oxidase- and oxygenase-catalyzed oxygen activation: a theoretical view

Oxygen plays a crucial role in the metabolic processes of non-anaerobic organisms. However, a detailed understanding of how triplet oxygen participates in the enzymatic oxidation of organic compounds involved in life processes is still lacking. It is noteworthy that recent studies have found that cofactor-free oxidase- and oxygenase-catalyzed oxygen activation occurs through proton-coupled electron transfer (PCET), which is significantly different from the previously proposed single electron transfer (SET) mechanism. Herein, we summarize the recent advances in the general mechanism of catalytic activation reactions of triplet oxygen by these enzymes. We believe that this review not only helps in providing a deep understanding of the processes involved in oxygen metabolism in organisms but also provides valuable theoretical reference data for designing more efficient enzyme mutants for treating diseases and handling environmental pollution in the future.

Unveiling the atlas of associations between 1,400 plasma metabolites and 24 tumors: Mendelian randomization analyses

Background

Association between plasma metabolites and pan-cancer remains controversial. Herein, we performed a two-sample Mendelian randomization (MR) analysis to verify whether there is a causal relationship between the two and to point the way for cancer metabolism research.

Methods

In our research, we downloaded 1,400 plasma metabolites from a large genome-wide association study (GWAS). We also obtained GWAS summary statistics for 24 types of cancers from the publicly available GWAS database, totaling 5,003,410 European individuals. We mainly used the fixed/random-effects inverse variance-weighted (IVW) method for two-sample MR analysis.

Results

In a combined sample of 291,202 cancer cases and 4,712,208 controls, a total of 55 plasma metabolites were identified as causally associated with nine types of cancer as a result of our MR analysis [P<0.05, false discovery rate (FDR) <0.2], including methionine sulfone, gamma-glutamylcitrulline, alliin, tetradecanedioate, hexadecanedioate, glutarate, ceramide, linolenoylcarnitine, hydroxypalmitoyl sphingomyelin, 1-palmitoyl-2-linoleoyl-glycerylphosphorylcholine (1-palmitoyl-2-linoleoyl-GPC), 3-acetylphenol sulfate, retinol (vitamin a) to linoleoyl-arachidonoyl-glycerol (18:2 to 20:4) ratio, etc. Reverse MR analysis revealed a causal relationship between lung cancer and the only plasma metabolite, 1-palmitoyl-2-linoleoyl-GPC (P<0.05, FDR <0.2).

Conclusions

Our study provides a comprehensive atlas of cancer-related plasma metabolites, offering possible targets for cancer detection, as well as a reference for future research on tumorigenesis mechanisms and therapeutic targets.

More than a colour; how pigment influences colourblind microbes

Many animals have pigments when they themselves cannot see colour. Perhaps those pigments enable the animal to avoid predators, or to attract mates. Maybe even those pigmented surfaces are hosts for microbes, even when the microbes do not see colour. Do some pigments then serve as a chemical signal for a good or bad microbial substrate? Maybe pigments attract or repel various microbe types? Echinoderms serve as an important model to test the mechanisms of pigment-based microbial interactions. Echinoderms are marine benthic organisms, ranging from intertidal habitats to depths of thousands of metres and are exposed to large varieties of microbes. They are also highly pigmented, with a diverse variety of colours between and even within species. Here we focus on one type of pigment (naphthoquinones) made by polyketide synthase, modified by flavin-dependent monoxygenases, and on one type of function, microbial interaction. Recent successes in targeted gene inactivation by CRISPR/Cas9 in sea urchins supports the contention that colour is more than it seems. Here we dissect the players, and their interactions to better understand how such host factors influence a microbial colonization. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.

The Promiscuous Flavin-Dependent Monooxygenase PboD from Aspergillus ustus Increases the Structural Diversity of Hydroxylated Pyrroloindoline Diketopiperazines

The potential of natural products as pharmaceutical and agricultural agents is based on their large structural diversity, resulting in part from modifications of the backbone structure by tailoring enzymes during biosynthesis. Flavin-dependent monooxygenases (FMOs), as one such group of enzymes, play an important role in the biosynthesis of diverse natural products, including cyclodipeptide (CDP) derivatives. The FMO PboD was shown to catalyze C-3 hydroxylation at the indole ring of cyclo-l-Trp-l-Leu in the biosynthesis of protubonines, accompanied by pyrrolidine ring formation. PboD substrate promiscuity was investigated in this study by testing its catalytic activity toward additional tryptophan-containing CDPs in vitro and biotransformation in Aspergillus nidulans transformants bearing a truncated protubonine gene cluster with pboD and two acetyltransferase genes. High acceptance of five CDPs was detected for PboD, especially of those with a second aromatic moiety. Isolation and structure elucidation of five pyrrolidine diketopiperazine products, with two new structures, proved the expected stereospecific hydroxylation and pyrrolidine ring formation. Determination of kinetic parameters revealed higher catalytic efficiency of PboD toward three CDPs consisting of aromatic amino acids than of its natural substrate cyclo-l-Trp-l-Leu. In the biotransformation experiments with the A. nidulans transformant, modest formation of hydroxylated and acetylated products was also detected.

Exploring the role of flavin-dependent monooxygenases in the biosynthesis of aromatic compounds

Hydroxylated aromatic compounds exhibit exceptional biological activities. In the biosynthesis of these compounds, three types of hydroxylases are commonly employed: cytochrome P450 (CYP450), pterin-dependent monooxygenase (PDM), and flavin-dependent monooxygenase (FDM). Among these, FDM is a preferred choice due to its small molecular weight, stable expression in both prokaryotic and eukaryotic fermentation systems, and a relatively high concentration of necessary cofactors. However, the catalytic efficiency of many FDMs falls short of meeting the demands of large-scale production. Additionally, challenges arise from the limited availability of cofactors and compatibility issues among enzyme components. Recently, significant progress has been achieved in improving its catalytic efficiency, but have not yet detailed and informative viewed so far. Therefore, this review emphasizes the advancements in FDMs for the biosynthesis of hydroxylated aromatic compounds and presents a summary of three strategies aimed at enhancing their catalytic efficiency: (a) Developing efficient enzyme mutants through protein engineering; (b) enhancing the supply and rapid circulation of critical cofactors; (c) facilitating cofactors delivery for enhancing FDMs catalytic efficiency. Furthermore, the current challenges and further perspectives on improving catalytic efficiency of FDMs are also discussed.

SQLE is a promising prognostic and immunological biomarker and correlated with immune Infiltration in Sarcoma

Squalene epoxidase (SQLE) is an essential enzyme involved in cholesterol biosynthesis. However, its role in sarcoma and its correlation with immune infiltration remains unclear. All original data were downloaded from The Cancer Genome Atlas (TCGA). SQLE expression was explored using the TCGA database, and correlations between SQLE and cancer immune characteristics were analyzed via the TISIDB databases. Generally, SQLE is predominantly overexpressed and has diagnostic and prognostic value in sarcoma. Upregulated SQLE was associated with poorer overall survival, poorer disease-specific survival, and tumor multifocality in sarcoma. Mechanistically, we identified a hub gene that included a total of 82 SQLE-related genes, which were tightly associated with histone modification pathways in sarcoma patients. SQLE expression was negatively correlated with infiltrating levels of dendritic cells and plasmacytoid dendritic cells and positively correlated with Th2 cells. SQLE expression was negatively correlated with the expression of chemokines (CCL19 and CX3CL1) and chemokine receptors (CCR2 and CCR7) in sarcoma. In conclusion, SQLE may be used as a prognostic biomarker for determining prognosis and immune infiltration in sarcoma.

Metabolic Engineering of Model Microorganisms for the Production of Xanthophyll

Xanthophyll is an oxidated version of carotenoid. It presents significant value to the pharmaceutical, food, and cosmetic industries due to its specific antioxidant activity and variety of colors. Chemical processing and conventional extraction from natural organisms are still the main sources of xanthophyll. However, the current industrial production model can no longer meet the demand for human health care, reducing petrochemical energy consumption and green sustainable development. With the swift development of genetic metabolic engineering, xanthophyll synthesis by the metabolic engineering of model microorganisms shows great application potential. At present, compared to carotenes such as lycopene and β-carotene, xanthophyll has a relatively low production in engineering microorganisms due to its stronger inherent antioxidation, relatively high polarity, and longer metabolic pathway. This review comprehensively summarized the progress in xanthophyll synthesis by the metabolic engineering of model microorganisms, described strategies to improve xanthophyll production in detail, and proposed the current challenges and future efforts needed to build commercialized xanthophyll-producing microorganisms.

Targeting the gut microbiota and its metabolites for type 2 diabetes mellitus

Type 2 diabetes mellitus (T2DM) is a metabolic disorder characterized by hyperglycemia and insulin resistance. The incidence of T2DM is increasing globally, and a growing body of evidence suggests that gut microbiota dysbiosis may contribute to the development of this disease. Gut microbiota-derived metabolites, including bile acids, lipopolysaccharide, trimethylamine-N-oxide, tryptophan and indole derivatives, and short-chain fatty acids, have been shown to be involved in the pathogenesis of T2DM, playing a key role in the host-microbe crosstalk. This review aims to summarize the molecular links between gut microbiota-derived metabolites and the pathogenesis of T2DM. Additionally, we review the potential therapy and treatments for T2DM using probiotics, prebiotics, fecal microbiota transplantation and other methods to modulate gut microbiota and its metabolites. Clinical trials investigating the role of gut microbiota and its metabolites have been critically discussed. This review highlights that targeting the gut microbiota and its metabolites could be a potential therapeutic strategy for the prevention and treatment of T2DM.

Editorial of Special Issue "Protective and Detrimental Role of Heme Oxygenase-1": 2021

The Special Issue "Protective and detrimental role of heme oxygenase-1"(2021), in the International Journal of Molecular Sciences, includes original research papers and reviews aiming to understand the protective or detrimental role of HO-1 and the signaling pathway involved [...].

Genomic Survey of Flavin Monooxygenases in Wild and Cultivated Rice Provides Insight into Evolution and Functional Diversities

The flavin monooxygenase (FMO) enzyme was discovered in mammalian liver cells that convert a carcinogenic compound, N-N'-dimethylaniline, into a non-carcinogenic compound, N-oxide. Since then, many FMOs have been reported in animal systems for their primary role in the detoxification of xenobiotic compounds. In plants, this family has diverged to perform varied functions like pathogen defense, auxin biosynthesis, and S-oxygenation of compounds. Only a few members of this family, primarily those involved in auxin biosynthesis, have been functionally characterized in plant species. Thus, the present study aims to identify all the members of the FMO family in 10 different wild and cultivated Oryza species. Genome-wide analysis of the FMO family in different Oryza species reveals that each species has multiple FMO members in its genome and that this family is conserved throughout evolution. Taking clues from its role in pathogen defense and its possible function in ROS scavenging, we have also assessed the involvement of this family in abiotic stresses. A detailed in silico expression analysis of the FMO family in Oryza sativa subsp. japonica revealed that only a subset of genes responds to different abiotic stresses. This is supported by the experimental validation of a few selected genes using qRT-PCR in stress-sensitive Oryza sativa subsp. indica and stress-sensitive wild rice Oryza nivara. The identification and comprehensive in silico analysis of FMO genes from different Oryza species carried out in this study will serve as the foundation for further structural and functional studies of FMO genes in rice as well as other crop types.

Current Progress in the Chemoenzymatic Synthesis of Natural Products

Natural products, with their array of structural complexity, diversity, and biological activity, have inspired generations of chemists and driven the advancement of techniques in their total syntheses. The field of natural product synthesis continuously evolves through the development of methodologies to improve stereoselectivity, yield, scalability, substrate scope, late-stage functionalization, and/or enable novel reactions. One of the more interesting and unique techniques to emerge in the last thirty years is the use of chemoenzymatic reactions in the synthesis of natural products. This review highlights some of the recent examples and progress in the chemoenzymatic synthesis of natural products from 2019–2022.

Plants' Physio-Biochemical and Phyto-Hormonal Responses to Alleviate the Adverse Effects of Drought Stress: A Comprehensive Review

Water, a necessary component of cell protoplasm, plays an essential role in supporting life on Earth; nevertheless, extreme changes in climatic conditions limit water availability, causing numerous issues, such as the current water-scarce regimes in many regions of the biome. This review aims to collect data from various published studies in the literature to understand and critically analyze plants' morphological, growth, yield, and physio-biochemical responses to drought stress and their potential to modulate and nullify the damaging effects of drought stress via activating natural physiological and biochemical mechanisms. In addition, the review described current breakthroughs in understanding how plant hormones influence drought stress responses and phytohormonal interaction through signaling under water stress regimes. The information for this review was systematically gathered from different global search engines and the scientific literature databases Science Direct, including Google Scholar, Web of Science, related studies, published books, and articles. Drought stress is a significant obstacle to meeting food demand for the world's constantly growing population. Plants cope with stress regimes through changes to cellular osmotic potential, water potential, and activation of natural defense systems in the form of antioxidant enzymes and accumulation of osmolytes including proteins, proline, glycine betaine, phenolic compounds, and soluble sugars. Phytohormones modulate developmental processes and signaling networks, which aid in acclimating plants to biotic and abiotic challenges and, consequently, their survival. Significant progress has been made for jasmonates, salicylic acid, and ethylene in identifying important components and understanding their roles in plant responses to abiotic stress. Other plant hormones, such as abscisic acid, auxin, gibberellic acid, brassinosteroids, and peptide hormones, have been linked to plant defense signaling pathways in various ways.

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.