Biochemical Characterization of CYP505D6, a Self-Sufficient Cytochrome P450 from the White-Rot Fungus Phanerochaete chrysosporium

Pathway crosstalk between the central metabolic and heme biosynthetic pathways in Phanerochaete chrysosporium

A comprehensive analysis to survey heme-binding proteins produced by the white-rot fungus Phanerochaete chrysosporium was achieved using a biotinylated heme-streptavidin beads system. Mitochondrial citrate synthase (PcCS), glyceraldehyde 3-phosphate dehydrogenase (PcGAPDH), and 2-Cys thioredoxin peroxidase (mammalian HBP23 homolog) were identified as putative heme-binding proteins. Among these, PcCS and PcGAPDH were further characterized using heterologously expressed recombinant proteins. Difference spectra of PcCS titrated with hemin exhibited an increase in the Soret absorbance at 414 nm, suggesting that the axial ligand of the heme is a His residue. The activity of PcCS was strongly inhibited by hemin with Ki oxaloacetate of 8.7 μM and Ki acetyl-CoA of 5.8 μM. Since the final step of heme biosynthesis occurred at the mitochondrial inner membrane, the inhibition of PcCS by heme is thought to be a physiological event. The inhibitory mode of the heme was similar to that of CoA analogues, suggesting that heme binds to PcCS at His347 at the AcCoA-CoA binding site, which was supported by the homology model of PcCS. PcGAPDH was also inhibited by heme, with a lower concentration than that for PcCS. This might be caused by the different location of these enzymes. From the integration of these phenomena, it was concluded that metabolic regulations by heme in the central metabolic and heme synthetic pathways occurred in the mitochondria and cytosol. This novel pathway crosstalk between the central metabolic and heme biosynthetic pathways, via a heme molecule, is important in regulating the metabolic balance (heme synthesis, ATP synthesis, flux balance of the tricarboxylic acid (TCA) cycle and cellular redox balance (NADPH production) during fungal aromatic degradation. KEY POINTS: • A comprehensive survey of heme-binding proteins in P. chrysosporium was achieved. • Several heme-binding proteins including CS and GAPDH were identified. • A novel metabolic regulation by heme in the central metabolic pathways was found.

Whole Genome Identification and Biochemical Characteristics of the Tilletia horrida Cytochrome P450 Gene Family

Rice kernel smut caused by the biotrophic basidiomycete fungus Tilletia horrida causes significant yield losses in hybrid rice-growing areas around the world. Cytochrome P450 (CYP) enzyme is a membrane-bound heme-containing monooxygenase. In fungi, CYPs play a role in cellular metabolism, adaptation, pathogenicity, decomposition, and biotransformation of hazardous chemicals. In this study, we identified 20 CYP genes based on complete sequence analysis and functional annotation from the T. horrida JY-521 genome. The subcellular localization, conserved motifs, and structures of these 20 CYP genes were further predicted. The ThCYP genes exhibit differences in gene structures and protein motifs. Subcellular localization showed that they were located in the plasma membrane, cytoplasm, nucleus, mitochondria, and extracellular space, indicating that they had multiple functions. Some cis-regulatory elements related to stress response and plant hormones were found in the promoter regions of these genes. Protein-protein interaction (PPI) analysis showed that several ThCYP proteins interact with multiple proteins involved in the ergosterol pathway. Moreover, the expression of 20 CYP genes had different responses to different infection time points and underwent dynamic changes during T. horrida JY-521 infection, indicating that these genes were involved in the interaction with rice and their potential role in the pathogenic mechanism. These results provided valuable resources for elucidating the structure of T. horrida CYP family proteins and laid an important foundation for further research of their roles in the pathogenesis.

Two Zn2Cys6-type transcription factors respond to aromatic compounds and regulate the expression of laccases in the white-rot fungus Trametes hirsuta

White-rot fungi differentially express laccases when they encounter aromatic compounds. However, the underlying mechanisms are still being explored. Here, proteomics analysis revealed that in addition to increased laccase activity, proteins involved in sphingolipid metabolism and toluene degradation as well as some cytochrome P450s (CYP450s) were differentially expressed and significantly enriched during 48 h of o-toluidine exposure, in Trametes hirsuta AH28-2. Two Zn2Cys6-type transcription factors (TFs), TH8421 and TH4300, were upregulated. Bioinformatics docking and isothermal titration calorimetry assays showed that each of them could bind directly to o-toluidine and another aromatic monomer, guaiacol. Binding to aromatic compounds promoted the formation of TH8421/TH4300 heterodimers. TH8421 and TH4300 silencing in T. hirsuta AH28-2 led to decreased transcriptional levels and activities of LacA and LacB upon o-toluidine and guaiacol exposure. EMSA and ChIP-qPCR analysis further showed that TH8421 and TH4300 bound directly with the promoter regions of lacA and lacB containing CGG or CCG motifs. Furthermore, the two TFs were involved in direct and positive regulation of the transcription of some CYP450s. Together, TH8421 and TH4300, two key regulators found in T. hirsuta AH28-2, function as heterodimers to simultaneously trigger the expression of downstream laccases and intracellular enzymes. Monomeric aromatic compounds act as ligands to promote heterodimer formation and enhance the transcriptional activities of the two TFs.IMPORTANCEWhite-rot fungi differentially express laccase isoenzymes when exposed to aromatic compounds. Clarification of the molecular mechanisms underlying differential laccase expression is essential to elucidate how white-rot fungi respond to the environment. Our study shows that two Zn2Cys6-type transcription factors form heterodimers, interact with the promoters of laccase genes, and positively regulate laccase transcription in Trametes hirsuta AH28-2. Aromatic monomer addition induces faster heterodimer formation and rate of activity. These findings not only identify two new transcription factors involved in fungal laccase transcription but also deepen our understanding of the mechanisms underlying the response to aromatics exposure in white-rot fungi.

Identification and characterization of methoxy- and dimethoxyhydroquinone 1,2-dioxygenase from Phanerochaete chrysosporium

White-rot fungi, such as Phanerochaete chrysosporium, are the most efficient degraders of lignin, a major component of plant biomass. Enzymes produced by these fungi, such as lignin peroxidases and manganese peroxidases, break down lignin polymers into various aromatic compounds based on guaiacyl, syringyl, and hydroxyphenyl units. These intermediates are further degraded, and the aromatic ring is cleaved by 1,2,4-trihydroxybenzene dioxygenases. This study aimed to characterize homogentisate dioxygenase (HGD)-like proteins from P. chrysosporium that are strongly induced by the G-unit fragment of vanillin. We overexpressed two homologous recombinant HGDs, PcHGD1 and PcHGD2, in Escherichia coli. Both PcHGD1 and PcHGD2 catalyzed the ring cleavage in methoxyhydroquinone (MHQ) and dimethoxyhydroquinone (DMHQ). The two enzymes had the highest catalytic efficiency (kcat/Km) for MHQ, and therefore, we named PcHGD1 and PcHGD2 as MHQ dioxygenases 1 and 2 (PcMHQD1 and PcMHQD2), respectively, from P. chrysosporium. This is the first study to identify and characterize MHQ and DMHQ dioxygenase activities in members of the HGD superfamily. These findings highlight the unique and broad substrate spectra of PcHGDs, rendering them attractive candidates for biotechnological applications.IMPORTANCEThis study aimed to elucidate the properties of enzymes responsible for degrading lignin, a dominant natural polymer in terrestrial lignocellulosic biomass. We focused on two homogentisate dioxygenase (HGD) homologs from the white-rot fungus, P. chrysosporium, and investigated their roles in the degradation of lignin-derived aromatic compounds. In the P. chrysosporium genome database, PcMHQD1 and PcMHQD2 were annotated as HGDs that could cleave the aromatic rings of methoxyhydroquinone (MHQ) and dimethoxyhydroquinone (DMHQ) with a preference for MHQ. These findings suggest that MHQD1 and/or MHQD2 play important roles in the degradation of lignin-derived aromatic compounds by P. chrysosporium. The preference of PcMHQDs for MHQ and DMHQ not only highlights their potential for biotechnological applications but also underscores their critical role in understanding lignin degradation by a representative of white-rot fungus, P. chrysosporium.

Microbial P450 repertoire (P450ome) and its application feasibility in pharmaceutical industry, chemical industry, and environmental protection

Cytochrome P450s (CYPs) are heme-thiolated enzymes that catalyze the oxidation of C-H bonds in a regio- and stereo-selective manner. CYPs are widely present in the biological world. With the completion of more biological genome sequencing, the number and types of P450 enzymes have increased rapidly. P450 in microorganisms is easy to clone and express, rich in catalytic types, and strong in substrate adaptability, which has good application potential. Although the number of P450 enzymes found in microorganisms is huge, the function of most of the microorganism P450s has not been studied, and it contains a large number of excellent biocatalysts to be developed. This review is based on the P450 groups in microorganisms. First, it reviews the distribution of P450 groups in different microbial species, and then studies the application of microbial P450 enzymes in the pharmaceutical industry, chemical industry and environmental pollutant treatment in recent years. And focused on the application fields of P450 enzymes of different families to guide the selection of suitable P450s from the huge P450 library. In view of the current shortcomings of microbial P450 in the application process, the final solution is the most likely to assist the application of P450 enzymes in large-scale, that is, whole cell transformation combined with engineering, fusion P450 combined with immobilization technology.

Various species of Basidiomycota fungi reveal different abilities to degrade pharmaceuticals and also different pathways of degradation

The presence of pharmaceuticals (PhACs) in the aquatic environment is an emerging problem worldwide. PhACs reach surface water via the effluents of wastewater treatment plants (WWTPs). WWTPs, although able to remove organic pollutants, do not always remove PhACs. Currently, in the treatment of sewage with the activated sludge method, numerous microorganisms are used, mostly bacteria. Nevertheless, these microorganisms are not resistant to many drug contaminants, and some may also pose a risk to human health. White-rot fungi (WRF), which degrade a wide spectrum of environmental pollutants, may be used as an alternative to microorganisms. However, little data exists comparing the removal of various PhACs by different WRF. In this study, we aimed to determine the ability of three WRF Basidiomycota species, Armillaria mellea, Phanerochaete chrysosporium, and Pleurotus ostreatus, to remove PhACs from various therapeutic groups over the course of 1 h-4 days. Additionally, we identified the fungal metabolites of PhACs, proposed the degradation pathways, and assessed the toxicity of the post-culture media. All selected WRF removed PhACs, but the degree of removal depended on WRF species and PhACs type. Antidepressants and immunosuppressants were removed most efficiently by P. ostreatus, cardiovascular drugs and sulfamethoxazole by A. mellea, and erythromycin by P. chrysosporium. The vast differences observed highlight the need for more intensive testing of different WRF species to select the best species for removing pharmaceuticals of interest. The structure of metabolites generated during degradation strongly depended on WRF species, but the most frequent xenobiotic transformations were oxidation and dealkylation. The obtained results gave insight into the substrate specificity of selected WRF while also providing a broad extension of the knowledge of pharmaceutical degradation by A. mellea.

Delineation of the CYP505E subfamily of fungal self-sufficient in-chain hydroxylating cytochrome P450 monooxygenases

Cytochrome P450 monooxygenases (CYP450s) are abundant in eukaryotes, specifically in plants and fungi where they play important roles in the synthesis and degradation of secondary metabolites. In eukaryotes, the best studied "self-sufficient" CYP450s, with a fused redox partner, belong to the CYP505 family. Members of the CYP505 family are generally considered sub-terminal fatty acid hydroxylases. CYP505E3 from Aspergillus terreus, however, gives remarkable in-chain hydroxylation at the ω-7 position of C10 to C16 alkanes and C12 and C14 fatty alcohols. Because CYP505E3 is a promising catalyst for the synthesis of δ-dodecalactone, we set out to delineate the unique ω-7 hydroxylase activity of CYP505E3. CYP505E3 and six additional CYP505Es as well as four closely related CYP505s from four different subfamilies were expressed in Pichia pastoris. Only the CYP505Es, sharing more than 70% amino acid identity, displayed significant ω-7 hydroxylase activity toward 1-dodecanol, dodecanoic acid, and tetradecanoic acid giving products that can readily be converted to δ-dodecalactone. Concentrations of δ-dodecalactone, directly extracted from dodecanoic acid biotransformations, were higher than previously obtained with E. coli. Searches of the UniProt and NCBI databases yielded a total of only 23 unique CYP505Es, all from the Aspergillaceae. Given that CYP505Es with this remarkable activity occur in only a few Aspergillus and Penicillium spp., we further explored the genetic environments in which they occur. These were found to be very distinct environments which include a specific ABC transporter but could not be linked to apparent secondary metabolite gene clusters. KEY POINTS: • Identified CYP505Es share > 70% amino acid identity. • CYP505Es hydroxylate 1-dodecanol, dodecanoic, and tetradecanoic acid at ω-7 position. • CYP505E genes occur in Aspergillus and Penicillium spp. near an ABC transporter.

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.

Biochemical characterization of hydroquinone hydroxylase from Phanerochaete chrysosporium

The white-rot fungus Phanerochaete chrysosporium can degrade lignin polymers using extracellular, non-specific, one-electron oxidizing enzymes. This results in the formation of guaiacyl (G), syringyl (S), and hydroxyphenyl (H) units, such as vanillic acid, syringic acid, and p-hydroxybenzoic acid (p-HBA) and the corresponding aldehydes, which are further metabolized intracellularly. Therefore, the aim of this study was to identify proteins involved in the hydroxylation of H-unit fragments such as p-HBA and its decarboxylated product hydroquinone (HQ) in P. chrysosporium. A flavoprotein monooxygenase (FPMO), PcFPMO2, was identified and its activity was characterized. Recombinant PcFPMO2 with an N-terminal polyhistidine tag was produced in Escherichia coli and purified. In the presence of NADPH, PcFPMO2 used six phenolic compounds as substrates. PcFPMO2 catalyzed the hydroxylation of the H-unit fragments such as p-HBA and HQ, and the G-unit derivative methoxyhydroquinone (MHQ). The highest catalytic efficiency (k_cat/K_m) was observed with HQ, indicating that PcFPMO2 could be involved in HQ hydroxylation in vivo. Additionally, PcFPMO2 converted MHQ to 3-, 5-, and 6-methoxy-1,2,4-trihydroxybenzene (3-, 5-, and 6-MTHB), respectively, suggesting that PcFPMO2 might partially be involved in MHQ degradation, following aromatic ring fission, via three MTHBs. FPMOs are divided into eight groups (groups A to H). This is the first study to show MHQ hydroxylase activity of a FPMO-group A superfamily member. These findings highlight the unique substrate spectrum of PcFPMO2, making it an attractive candidate for biotechnological applications.

Bioremediation of organic pollutants by white rot fungal cytochrome P450: The role and mechanism of CYP450 in biodegradation

Cytochrome P450 (CYP450) is a well-known protein family that is widely distributed in many organisms. Members of this family have been implicated in a broad range of reactions involved in the metabolism of various organic compounds. Recently, an increasing number of studies have shown that the CYP450 enzyme also participates in the elimination and degradation of organic pollutants, by white rot fungi (WRF), a famous group of natural degraders. This paper reviews previous investigations of white rot fungal CYP450 involved in the biodegradation of organic pollutants, with a special focus on inhibitory experiments, and the direct and indirect evidence of the role of white rot fungal CYP450 in bioremediation. The catalytic mechanisms of white rot fungal CYP450, its application potential, and future prospect for its use in bioremediation are then discussed.

Characterization of two 1,2,4-trihydroxybenzene 1,2-dioxygenases from Phanerochaete chrysosporium

Lignin is the most abundant aromatic compound in nature, and it plays an important role in the carbon cycle. White-rot fungi are microbes that are capable of efficiently degrading lignin. Enzymes from these fungi possess exceptional oxidative potential and have gained increasing importance for improving bioprocesses, such as the degradation of organic pollutants. The aim of this study was to identify the enzymes involved in the ring cleavage of the lignin-derived aromatic 1,2,4-trihydroxybenzene (THB) in Phanerochaete chrysosporium, a lignin-degrading basidiomycete. Two intradiol dioxygenases (IDDs), PcIDD1 and PcIDD2, were identified and produced as recombinant proteins in Escherichia coli. In the presence of O₂, PcIDD1 and PcIDD2 acted on eight and two THB derivatives, respectively, as substrates. PcIDD1 and PcIDD2 catalyze the ring cleavage of lignin-derived fragments, such as 6-methoxy-1,2,4-trihydroxybenzene (6-MeOTHB) and 3-methoxy-1,2-catechol. The current study also revealed that syringic acid (SA) was converted to 5-hydroxyvanillic acid, 2,6-dimethoxyhydroquinone, and 6-MeOTHB by fungal cells, suggesting that PcIDD1 and PcIDD2 may be involved in aromatic ring fission of 6-MeOTHB for SA degradation. This is the first study to show 6-MeOTHB dioxygenase activity of an IDD superfamily member. These findings highlight the unique and broad substrate spectra of PcIDDs, rendering it an attractive candidate for biotechnological application. KEY POINTS: • Novel intradiol dioxygenases (IDD) in lignin degradation were characterized. • PcIDDs acted on lignin-derived fragments and catechol derivatives. • Dioxygenase activity on 6-MeOTHB was identified in IDD superfamily enzymes.

Enhanced Bioremediation of 4-Chlorophenol by Electrically Neutral Reactive Species Generated from Nonthermal Atmospheric-Pressure Plasma

4-Chlorophenol (4-CP) is a chlorinated aromatic compound with broad industrial applications. It is released into the environment as an industrial byproduct and is highly resistant to biodegradation. Pseudomonas sp. in the environment and activated sludge are used for 4-CP bioremediation; however, the degradation of 4-CP takes a long time. Consequently, the toxicity of 4-CP is a major barrier to its bioremediation. In this study, we investigated the synergistic effect of electrically neutral reactive species on the bacterial bioremediation of 4-CP. Our results showed that the concentration of 4-CP decreased from 2.0 to 0.137 mM and that it was converted to 4-chlorocatechol (4-CC; 0.257 mM), 4-chlororesorcinol (0.157 mM), hydroquinone (0.155 mM), and trihydroxy chlorobenzene and their respective ring-cleaved products following irradiation of neutral reactive species. These compounds were less toxic than 4-CP, except for 4-CC, which reduced the toxicity of 4-CP to Pseudomonas putida. When the neutral reactive species-treated 4-CP fraction was added to P. putida cultured in a synthetic sewage medium for 48 h, the 4-CP concentration was reduced to 0.017 mM, whereas nontreated 4-CP (2.0 mM) was hardly degraded by P. putida. These results suggest that the biodegradation of 4-CP can be efficiently improved by combining irradiation of neutral reactive species with microbial treatment. The irradiation of neutral reactive species of environmental pollutants may additionally lead to further improvements in bioremediation processes.

Latent Functions and Applications of Cytochrome P450 Monooxygenases from Thamnidium elegans: A Novel Biocatalyst for 14α-Hydroxylation of Testosterone

Cytochrome P450 monooxygenases (P450s) are ubiquitous enzymes with high availability and diversity in nature. Fungi provide a diverse and complex array of P450s, and these enzymes play essential roles in various secondary metabolic processes. Besides the physiological impacts of P450s on fungal life, their versatile functions are attractive for use in advanced applications of the biotechnology sector. Herein, we report gene identification and functional characterization of P450s from the zygomycetous fungus Thamnidium elegans (TeCYPs). We identified 48 TeCYP genes, including two putative pseudogenes, from the whole-genome sequence of T. elegans. Furthermore, we constructed a functional library of TeCYPs and heterologously expressed 46 TeCYPs in Saccharomyces cerevisiae. Recombinants of S. cerevisiae were then used as whole-cell biocatalysts for bioconversion of various compounds. Catalytic potentials of various TeCYPs were demonstrated through a functionomic survey to convert a series of compounds, including steroidal substrates. Notably, CYP5312A4 was found to be highly active against testosterone. Based on nuclear magnetic resonance analysis, enzymatic conversion of testosterone to 14α-hydroxytestosterone by CYP5312A4 was demonstrated. This is the first report to identify a novel fungal P450 that catalyzes the 14α-hydroxylation of testosterone. In addition, we explored the latent potentials of TeCYPs using various substrates. This study provides a platform to further study the potential use of TeCYPs as catalysts in pharmaceutical and agricultural industries and biotechnology.

Optimization of White-Rot Fungi Mycelial Culture Components for Bioremediation of Pharmaceutical-Derived Pollutants

White-rot fungi can degrade a wide spectrum of environmental pollutants, including pharmaceuticals, which are not efficiently removed from wastewater by conventional methods, e.g., the activated sludge method. However, the treatment of wastewater with the use of fungal cultures (mycoremediation) also has significant limitations: among others, the need to use appropriate, often-expensive culture media. We aimed to screen 18 media ingredients, including seven agrifood byproducts for Armillaria mellea, Phanerochaete chrysosporium and Pleurotus ostreatus in submerged cultures to select the low-cost medium optimal for biomass production and laccase activity. We screened nine mathematic models to describe the relation of fungal growth and the amount of the selected byproduct in media. Finally, we tested the ability of the strain with the highest mycelial growth and enzyme-producing ability in the selected medium to degrade eight drug contaminants. Three media variants composed of byproducts provided both efficient growth and laccase production: corn steep liquor + poplar, dried distillers grains with solubles + poplar and corn steep liquor 50%. Among the investigated growth models, the Han–Levenspiel equation described well the specific growth rate in function of the nominal substrate concentration in one-component media. Pleurotus ostreatus, the fungus with the highest ligninolytic enzyme activity, cultured in medium composed of corn steep liquor, removed six of eight drug contaminants with a removal degree of 20–90% in 48 h. The obtained data on the optimal culture media consisting of insoluble components provide initial data for upscaling the process and designing an appropriate type of bioreactor for the process of removing drug contaminants from water.

Late-Stage Functionalisation of Polycyclic (N-Hetero-) Aromatic Hydrocarbons by Detoxifying CYP5035S7 Monooxygenase of the White-Rot Fungus Polyporus arcularius

Functionalisation of polycyclic aromatic hydrocarbons (PAHs) and their N-heteroarene analogues (NPAHs) is a tedious synthetic endeavour that requires diverse bottom-up approaches. Cytochrome P450 enzymes of white-rot fungi were shown to participate in the fungal detoxification of xenobiotics and environmental hazards via hydroxylation of PAH compounds. In this paper, the recently discovered activity of the monooxygenase CYP5035S7 towards (N)PAHs was investigated in detail, and products formed from the substrates azulene, acenaphthene, fluorene, anthracene, and phenanthrene by whole-cell biocatalysis were isolated and characterised. The observed regioselectivity of CYP5035S7 could be explained by a combination of the substrate's electron density and steric factors influencing the substrate orientation giving insight into the active-site geometry of the enzyme.

Biosynthesis and regulation of terpenoids from basidiomycetes: exploration of new research

Basidiomycetes, also known as club fungi, consist of a specific group of fungi. Basidiomycetes produce a large number of secondary metabolites, of which sesquiterpenoids, diterpenoids and triterpenoids are the primary components. However, these terpenoids tend to be present in low amounts, which makes it difficult to meet application requirements. Terpenoid biosynthesis improves the quantity of these secondary metabolites. However, current understanding of the biosynthetic mechanism of terpenoids in basidiomycetes is insufficient. Therefore, this article reviews the latest research on the biosynthesis of terpenoids in basidiomycetes and summarizes the CYP450 involved in the biosynthesis of terpenoids in basidiomycetes. We also propose opportunities and challenges for chassis microbial heterologous production of terpenoids in basidiomycetes and provide a reference basis for the better development of basidiomycete engineering.

Evolution and enrichment of CYP5035 in Polyporales: functionality of an understudied P450 family

Abstract

Bioprospecting for innovative basidiomycete cytochrome P450 enzymes (P450s) is highly desirable due to the fungi’s enormous enzymatic repertoire and outstanding ability to degrade lignin and detoxify various xenobiotics. While fungal metagenomics is progressing rapidly, the biocatalytic potential of the majority of these annotated P450 sequences usually remains concealed, although functional profiling identified several P450 families with versatile substrate scopes towards various natural products. Functional knowledge about the CYP5035 family, for example, is largely insufficient. In this study, the families of the putative P450 sequences of the four white-rot fungi Polyporus arcularius, Polyporus brumalis, Polyporus squamosus and Lentinus tigrinus were assigned, and the CYPomes revealed an unusual enrichment of CYP5035, CYP5136 and CYP5150. By computational analysis of the phylogeny of the former two P450 families, the evolution of their enrichment could be traced back to the Ganoderma macrofungus, indicating their evolutionary benefit. In order to address the knowledge gap on CYP5035 functionality, a representative subgroup of this P450 family of P. arcularius was expressed and screened against a test set of substrates. Thereby, the multifunctional enzyme CYP5035S7 converting several plant natural product classes was discovered. Aligning CYP5035S7 to 102,000 putative P450 sequences of 36 fungal species from Joint Genome Institute-provided genomes located hundreds of further CYP5035 family members, which subfamilies were classified if possible. Exemplified by these specific enzyme analyses, this study gives valuable hints for future bioprospecting of such xenobiotic-detoxifying P450s and for the identification of their biocatalytic potential.

Graphical abstract

Key points

• The P450 families CYP5035 and CYP5136 are unusually enriched in P. arcularius.

• Functional screening shows CYP5035 assisting in the fungal detoxification mechanism.

• Some Polyporales encompass an unusually large repertoire of detoxification P450s.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11444-2.

A comprehensive insight into the application of white rot fungi and their lignocellulolytic enzymes in the removal of organic pollutants

Environmental problems resultant from organic pollutants are a major current challenge for modern societies. White rot fungi (WRF) are well known for their extensive organic compound degradation abilities. The unique oxidative and extracellular ligninolytic systems of WRF that exhibit low substrate specificity, enable them to display a considerable ability to transform or degrade different environmental contaminants. In recent decades, WRF and their ligninolytic enzymes have been widely applied in the removal of polycyclic aromatic hydrocarbons (PAHs), pharmaceutically active compounds (PhACs), endocrine disruptor compounds (EDCs), pesticides, synthetic dyes, and other environmental pollutants, wherein promising results have been achieved. This review focuses on advances in WRF-based bioremediation of organic pollutants over the last 10 years. We comprehensively document the application of WRF and their lignocellulolytic enzymes for removing organic pollutants. Moreover, potential problems and intriguing observations that are worthy of additional research attention are highlighted. Lastly, we discuss trends in WRF-remediation system development and avenues that should be considered to advance research in the field.

P450-driven plastic-degrading synthetic bacteria

Plastic contamination currently threatens a wide variety of ecosystems and presents damaging repercussions and negative consequences for many wildlife species. Sustainable plastic waste management is an important approach to environmental protection and a necessity in the current life cycle of plastics in nature. Plastic biodegradation by microorganisms is a notable possible solution. This opinion article includes a proposal to use hypothetical P450 enzymes with an engineered active site as potent trigger biocatalysts to biodegrade polyethylene (PE) via in-chain hydroxylation into smaller products of linear aliphatic alcohols and alkanoic acids based on cascade enzymatic reactions. Furthermore, we propose the adoption of P450 into plastic-eating synthetic bacteria for PE biodegradation. This strategy can be applicable to other dense plastics, such as polypropylene (PP) and polystyrene (PS).

Biocatalytic synthesis of non-vicinal aliphatic diols

Biocatalysts are receiving increased attention in the field of selective oxyfunctionalization of C-H bonds, with cytochrome P450 monooxygenases (CYP450s), and the related peroxygenases, leading the field. Here we report on the substrate promiscuity of CYP505A30, previously characterized as a fatty acid hydroxylase. In addition to its regioselective oxyfunctionalization of saturated fatty acids (ω-1 - ω-3 hydroxylation), primary fatty alcohols are also accepted with similar regioselectivities. Moreover, alkanes such as n-octane and n-decane are also readily accepted, allowing for the production of non-vicinal diols through sequential oxygenation.

Structure of the fungal hydroxylase, CYP505A30, and rational transfer of mutation data from CYP102A1 to alter regioselectivity

Regioselective oxyfunctionalisation of n-alkanes and production of non-vicinal diols by evolved CYP505A30 through rational transfer of knowledge between protein scaffolds.

Characterization of FsXEG12A from the cellulose-degrading ectosymbiotic fungus Fusarium spp. strain EI cultured by the ambrosia beetle

Despite the threat of Fusarium dieback posed due to ambrosia fungi cultured by ambrosia beetles such as Euwallacea spp., the wood-degradation mechanisms utilized by ambrosia fungi are not fully understood. In this study, we analyzed the 16S rRNA and 18S rRNA genes of the microbial community from the Ficus tree tunnel excavated by Euwallacea interjectus and isolated the cellulose-degrading fungus, Fusarium spp. strain EI, by enrichment culture with carboxymethyl cellulose as the sole carbon source. The cellulolytic enzyme secreted by the fungus was identified and expressed in Pichia pastoris, and its enzymatic properties were characterized. The cellulolytic enzyme, termed FsXEG12A, could hydrolyze carboxymethyl cellulose, microcrystalline cellulose, xyloglucan, lichenan, and glucomannan, indicating that the broad substrate specificity of FsXEG12A could be beneficial for degrading complex wood components such as cellulose, xyloglucan, and galactoglucomannan in angiosperms. Inhibition of FsXEG12A function is, thus, an effective target for Fusarium dieback caused by Euwallacea spp.

Characterization of a Self-Sufficient Cytochrome P450 Monooxygenase from Deinococcus apachensis for Enantioselective Benzylic Hydroxylation

A self-sufficient cytochrome P450 monooxygenase from Deinococcus apachensis (P450DA) was identified and successfully overexpressed in Escherichia coli BL21(DE3). P450DA would be a member of the CYP102D subfamily and assigned as CYP102D2 according to the phylogenetic tree and sequence alignment. Purification and characterization of the recombinant P450DA indicated both NADH and NADPH could be used by P450DA as a reducing cofactor. The recombinant E. coli (P450DA) strain was functionally active, showing excellent enantioselectivity for benzylic hydroxylation of methyl 2-phenylacetate. Further substrate scope studies revealed that P450DA is able to catalyze benzylic hydroxylation of a variety of compounds, affording the corresponding chiral benzylic alcohols in 86-99 % ee and 130-1020 total turnover numbers.

Oxygen radical based on non-thermal atmospheric pressure plasma alleviates lignin-derived phenolic toxicity in yeast

BACKGROUND

Vanillin is the main byproduct of alkaline-pretreated lignocellulosic biomass during the process of fermentable-sugar production and a potent inhibitor of ethanol production by yeast. Yeast cells are usually exposed to vanillin during the industrial production of bioethanol from lignocellulosic biomass. Therefore, vanillin toxicity represents a major barrier to reducing the cost of bioethanol production.

RESULTS

In this study, we analysed the effects of oxygen-radical treatment on vanillin molecules. Our results showed that vanillin was converted to vanillic acid, protocatechuic aldehyde, protocatechuic acid, methoxyhydroquinone, 3,4-dihydroxy-5-methoxybenzaldehyde, trihydroxy-5-methoxybenzene, and their respective ring-cleaved products, which displayed decreased toxicity relative to vanillin and resulted in reduced vanillin-specific toxicity to yeast during ethanol fermentation. Additionally, after a 16-h incubation, the ethanol concentration in oxygen-radical-treated vanillin solution was 7.0-fold greater than that from non-treated solution, with similar results observed using alkaline-pretreated rice straw slurry with oxygen-radical treatment.

CONCLUSIONS

This study analysed the effects of oxygen-radical treatment on vanillin molecules in the alkaline-pretreated rice straw slurry, thereby finding that this treatment converted vanillin to its derivatives, resulting in reduced vanillin toxicity to yeast during ethanol fermentation. These findings suggest that a combination of chemical and oxygen-radical treatment improved ethanol production using yeast cells, and that oxygen-radical treatment of plant biomass offers great promise for further improvements in bioethanol-production processes.