Cytochrome P450 5208A3 is a promiscuous xenobiotic biotransforming enzyme in Cunninghamella elegans

Functional Expression and Construction of a Self-Sufficient Cytochrome P450 Chimera for Efficient Steroidal C14α Hydroxylation in Escherichia coli

C14-functionalized steroids enabled diverse biological activities in anti-gonadotropin and anticancer therapy. However, access to C14-functionalized steroids was impeded by the deficiency of chemical synthetic methods. Recently, several membrane-bound fungal cytochrome P450s (CYPs) have been identified with steroid C14α-hydroxylation activity. However, the lack of efficient heterologous overexpression strategy hampered their further characterization and molecular engineering. In the present study, sequences of fungi-derived CYP genes encoding putative 14α-hydroxylase were selected and bioinformatically analyzed. Substitution of the N-terminal hydrophobic helix by a soluble maltose binding protein tag significantly enhanced the soluble expression level in Escherichia coli. A novel CYP originated from Bipolaris oryzae was discovered with high steroidal C14α-hydroxylation activity when coupled with the redox partner CPRlun. A catalytically self-sufficient chimeric CYP-CPR was built by intramolecular fusion, and the electronic transfer rate was improved. A coenzyme NADPH regeneration system was finally constructed by the co-expression of glucose dehydrogenase. The developed soluble multi-enzyme cascade biotransformation system supported the selective C14α-hydroxylation toward progesterone with a final titer of 34.54 mg/L, the highest level achieved in E. coli-based heterologous expression system. This study provides insightful ideas on the functional expression of fungi-derived CYPs and promises an efficient C14α-hydroxylation system for steroidal drugs through protein engineering.

A Computational Pipeline Observes the Flexibility and Dynamics of Plant Cytochrome P450 Binding Sites

Binding site flexibility and dynamics strongly affect the ability of proteins to accommodate substrates and inhibitors. The significance of these properties is particularly pronounced for proteins that are inherently flexible, such as cytochrome P450 enzymes (CYPs). While the research on human CYPs provides detailed knowledge on both structural and functional level, such analyses are still lacking for their plant counterparts. This study aims to bridge this gap. We developed a novel computational pipeline consisting of two steps. Firstly, we use molecular dynamics (MD) simulations to capture the full conformational ensemble for a certain plant CYP. Subsequently, we developed and applied a comprehensive methodology to analyze a number of binding site properties-size, flexibility, shape, hydrophobicity, and accessibility-using the fpocket and mdpocket packages on MD-generated trajectories. The workflow was validated on human CYPs 1A2, 2A6, and 3A4, as their binding site characteristics are well known. Not only could we confirm known binding site properties, but we also identified and named previously unseen binding site channels for CYPs 1A2 and 2A6. The pipeline was then applied to plant CYPs, leading to the first categorization of 15 chosen plant CYPs based on their binding site's (dis)similarities. This study provides a foundation for the largely uncharted fields of plant CYP substrate specificity and facilitates a more precise understanding of their largely unknown specific biological functions. It offers new insights into the structural and functional dynamics of plant CYPs, which may facilitate a more accurate understanding of the fate of agrochemicals or the biotechnological design and exploitation of enzymes with specific functions. Additionally, it serves as a reference for future structural-functional analyses of CYP enzymes across various biological kingdoms.

Pharmaceutical removal from wastewater by introducing cytochrome P450s into microalgae

Pharmaceuticals are of increasing environmental concern as they emerge and accumulate in surface- and groundwater systems around the world, endangering the overall health of aquatic ecosystems. Municipal wastewater discharge is a significant vector for pharmaceuticals and their metabolites to enter surface waters as humans incompletely absorb prescription drugs and excrete up to 50% into wastewater, which are subsequently incompletely removed during wastewater treatment. Microalgae present a promising target for improving wastewater treatment due to their ability to remove some pollutants efficiently. However, their inherent metabolic pathways limit their capacity to degrade more recalcitrant organic compounds such as pharmaceuticals. The human liver employs enzymes to break down and absorb drugs, and these enzymes are extensively researched during drug development, meaning the cytochrome P450 enzymes responsible for metabolizing each approved drug are well studied. Thus, unlocking or increasing cytochrome P450 expression in endogenous wastewater microalgae could be a cost-effective strategy to reduce pharmaceutical loads in effluents. Here, we discuss the challenges and opportunities associated with introducing cytochrome P450 enzymes into microalgae. We anticipate that cytochrome P450-engineered microalgae can serve as a new drug removal method and a sustainable solution that can upgrade wastewater treatment facilities to function as "mega livers".

Dissecting the genome sequence of a clinical isolated Cunninghamella bertholletiae Z2 strain with rich cytochrome P450 enzymes (Article)

Mucormycosis is receiving much more attention because of its high morbidity and extremely high mortality rate in immunosuppressed populations. In this study, we isolated a Cunnignhamella bertholletiae Z2 strain from a skin lesion of a 14 year, 9 months old girl with acute lymphoblastic leukemia who die of infection from the Z2 strain. Genome sequencing was performed after isolation and amplification of the Z2 strain to reveal potential virulence factors and pathogenic mechanisms. The results showed that the genome size of the Z2 strain is 30.9 Mb with 9213 genes. Mucoral specific virulence factor genes found are ARF, CalN, and CoTH, while no gliotoxin biosynthesis gene cluster was found, which is a known virulence factor in Aspergillus fumigatus adapted to the environment. The Z2 strain was found to have 69 cytochrome P450 enzymes, which are potential drug resistant targets. Sensitivity testing of Z2 showed it was only inhibited by amphotericin B and posaconazole. Detailed genomic information of the C. bertholletiae Z2 strain may provide useful data for treatment.

Toward the development of a molecular toolkit for the microbial remediation of per-and polyfluoroalkyl substances

Per- and polyfluoroalkyl substances (PFAS) are highly fluorinated synthetic organic compounds that have been used extensively in various industries owing to their unique properties. The PFAS family encompasses diverse classes, with only a fraction being commercially relevant. These substances are found in the environment, including in water sources, soil, and wildlife, leading to human exposure and fueling concerns about potential human health impacts. Although PFAS degradation is challenging, biodegradation offers a promising, eco-friendly solution. Biodegradation has been effective for a variety of organic contaminants but is yet to be successful for PFAS due to a paucity of identified microbial species capable of transforming these compounds. Recent studies have investigated PFAS biotransformation and fluoride release; however, the number of specific microorganisms and enzymes with demonstrable activity with PFAS remains limited. This review discusses enzymes that could be used in PFAS metabolism, including haloacid dehalogenases, reductive dehalogenases, cytochromes P450, alkane and butane monooxygenases, peroxidases, laccases, desulfonases, and the mechanisms of microbial resistance to intracellular fluoride. Finally, we emphasize the potential of enzyme and microbial engineering to advance PFAS degradation strategies and provide insights for future research in this field.

Pure lignin induces overexpression of cytochrome P450 (CYP) encoding genes and brings insights into the lignocellulose depolymerization by Trametes villosa

Trametes villosa is a remarkable white-rot fungus (WRF) with the potential to be applied in lignocellulose conversion to obtain chemical compounds and biofuels. Lignocellulose breakdown by WRF is carried out through the secretion of oxidative and hydrolytic enzymes. Despite the existing knowledge about this process, the complete molecular mechanisms involved in the regulation of this metabolic system have not yet been elucidated. Therefore, in order to understand the genes and metabolic pathways regulated during lignocellulose degradation, the strain T. villosa CCMB561 was cultured in media with different carbon sources (lignin, sugarcane bagasse, and malt extract). Subsequently, biochemical assays and differential gene expression analysis by qPCR and high-throughput RNA sequencing were carried out. Our results revealed the ability of T. villosa CCMB561 to grow on lignin (AL medium) as the unique carbon source. An overexpression of Cytochrome P450 was detected in this medium, which may be associated with the lignin O-demethylation pathway. Clusters of up-regulated CAZymes-encoding genes were identified in lignin and sugarcane bagasse, revealing that T. villosa CCMB561 acts simultaneously in the depolymerization of lignin, cellulose, hemicellulose, and pectin. Furthermore, genes encoding nitroreductases and homogentisate-1,2-dioxygenase that act in the degradation of organic pollutants were up-regulated in the lignin medium. Altogether, these findings provide new insights into the mechanisms of lignocellulose degradation by T. villosa and confirm the ability of this fungal species to be applied in biorefineries and in the bioremediation of organic pollutants.

Biotransformation of fluorinated drugs and xenobiotics by the model fungus Cunninghamella elegans

Some species of the genus Cunninghamella (C. elegans, C. echinulata and C. blaskesleeana) produce the same phase I and phase II metabolites when incubated with xenobiotics as mammals, and thus are considered microbial models of mammalian metabolism. This had made these fungi attractive for metabolism studies with drugs, pesticides and environmental pollutants. As a substantial proportion of pharmaceuticals and agrochemicals are fluorinated, their biotransformation has been studied in Cunninghamella fungi and C. elegans in particular. This article details the methods employed for cultivating the fungi in planktonic and biofilm cultures, and extraction and analysis of fluorinated metabolites. Furthermore, protocols for the heterologous expression of Cunninghamella cytochromes P450 (CYPs), which are the enzymes associated with phase I metabolism, are described.

In silico and in vitro evaluation of a safety profile of a cosmetic ingredient: 4-methoxychalcone (4-MC)

Chalcone is an important scaffold within medicinal and cosmetic chemistry. The structure enables multiple modifications which may result in obtaining compounds with desirable bioactivity. One of the chalcone derivatives, 4-methoxychalcone is a known cosmetic ingredient indexed in Cosing database as an antioxidant, bleaching, and skin conditioning substance. We investigated its in silico and in vitro safety profile. In silico study using Derek Nexus showed its potential of skin sensitisation, equivocal nature of chromosome damage in vitro in mammals, but also no mutagenic properties. In vitro research proved its activity as melanogenesis inhibitor in B16F10 cell line at the doses 12.5-3.125 μM. Evaluations performed in various cell lines showed that the cytotoxic doses were 50-25 μM. Tests in Episkin™ proved its ability to penetrate across epidermis and enabled classification of 2% formulation in PEG as non-irritant. In micronucleus tests it showed no genotoxicity. Studies in Cunninghamella echinulata model proved that 4-methoxychalcone was metabolised to less lipophilic products. 4-methoxychalcone showed phototoxic potential, its EC50(+UV) = 3.57 μg/mL, PIF = 10.19 and MPE = 0.428 were comparable to chlorpromazine. Moreover, 4-methoxychalcone showed ecotoxic potential in Microtox® assay with EC50(5 min) = 0.0047 mg/L and EC50(15 min) = 0.0033 mg/L. Although active doses were lower than toxic ones, some potential safety risks were noticed. Especially, due to the phototoxicity potential of 4-methoxychalcone, its use as depigmenting agent should involve avoidance of sunlight and use of appropriate photoprotection.

Metabolism of natural and synthetic bioactive compounds in Cunninghamella fungi and their applications in drug discovery

Investigation of xenobiotic metabolism is a key step for drug discovery. Since the in vivo investigations may be associated with harmful effects attributed to production of toxic metabolites, it is deemed necessary to predict their structure especially at the preliminary clinical studies. Furthermore, the application of microorganisms that are capable of metabolizing drugs mimic human metabolism and consequently may predict possible metabolites. The genus Cunninghamella has been proven to be a potential candidate, which mimics xenobiotic metabolism occurring inside the human body, including phase I and II metabolic reactions. Moreover, biotransformation with Cunninghamella showed chemical diversity, where a lot of products were detected in relation to the initial substrates after being modified by oxidation, hydroxylation, and conjugation reactions. Some of these products are more bioactive than the parent compounds. The current review presents a comprehensive literature overview regarding the Cunninghamella organisms as biocatalysts, which simulate mammalian metabolism of natural secondary and synthetic compounds.

Endogenous production of 2-phenylethanol by Cunninghamella echinulata inhibits biofilm growth of the fungus

The filamentous fungus Cunninghamella echinulata is a model of mammalian xenobiotic metabolism. Under certain conditions it grows as a biofilm, which is a natural form of immobilisation and enables the fungus to catalyse repeated biotransformations. Putative signalling molecules produced by other Cunninghamella spp., such as 3-hydroxytyrosol and tyrosol, do not affect the biofilm growth of C. echinulata, suggesting that it employs a different molecule to regulate biofilm growth. In this paper we report that 2-phenylethanol is produced in higher concentrations in planktonic cultures of C. echinulata than when the fungus is grown as a biofilm. We demonstrate that exogenously added 2-phenylethanol inhibits biofilm growth of C. echinulata but has no effect on planktonic growth. Furthermore, we show that addition of 2-phenylethanol to established C. echinulata biofilm causes detachment. Therefore, we conclude that this molecule is produced by the fungus to regulate biofilm growth.

Recent advances in fungal xenobiotic metabolism: enzymes and applications

Fungi have been extensively studied for their capacity to biotransform a wide range of natural and xenobiotic compounds. This versatility is a reflection of the broad substrate specificity of fungal enzymes such as laccases, peroxidases and cytochromes P450, which are involved in these reactions. This review gives an account of recent advances in the understanding of fungal metabolism of drugs and pollutants such as dyes, agrochemicals and per- and poly-fluorinated alkyl substances (PFAS), and describes the key enzymes involved in xenobiotic biotransformation. The potential of fungi and their enzymes in the bioremediation of polluted environments and in the biocatalytic production of important compounds is also discussed.

Fluorotelomer alcohols are efficiently biotransformed by Cunninghamella elegans

Cunninghamella elegans is a well-studied fungus that biotransforms a range of xenobiotics owing to impressive cytochrome P450 (CYP) activity. In this paper, we report the biotransformation of 6:2 fluorotelomer alcohol (6:2 FTOH) by the fungus, yielding a range of fluorinated products that were detectable by fluorine-19 nuclear magnetic resonance spectroscopy (¹⁹F NMR), gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS). Upon incubation with the pre-grown cultures, the substrate (100 mg/L) was completely consumed within 48 h, which is faster biotransformation than other fungi that have hitherto been studied. The main metabolite formed was the 5:3 fluorotelomer carboxylic acid (5:3 FTCA), which accumulated in the culture supernatant. When the cytochrome P450 inhibitor 1-aminobenzotriazole was included in the culture flasks, there was no biotransformation of 6:2 FTOH, indicating that these enzymes are key to the catalysis. Furthermore, when exogenous 5:3 FTCA was added to the fungus, the standard biotransformation of the drug flurbiprofen was inhibited, strongly suggesting that the main fluorotelomer alcohol biotransformation product inhibits CYP activity and accounts for its accumulation.

An O-Demethylation Metabolite of Rabeprazole Sulfide by Cunninghamella blakesleeana 3.970 Biotransformation

To explore the potential metabolites from rabeprazole sulfide, seven strains of filamentous fungi were screened for their biotransformation abilities. Among these strains, Cunninghamella blakesleeana 3.970 exhibited the best result. Four different culture media were screened in order to identify the most optimal for subsequent research. Single factors such as the initial pH of culture media, culture time, inoculation volume, and media volume were individually investigated to provide the optimum biotransformation conditions. Then, an orthogonal optimization process using a five-factor, four-level L16(45) experiment was designed and performed. Finally, when the substrate concentration is 3 g/L, one major metabolite was detected with a transformation rate of 72.4%. Isolated by semipreparative HPLC, this metabolite was further detected by ESI-MS and NMR. The final data analysis indicated that the metabolite is O-demethylation rabeprazole sulfide.