Benzene oxygenation and oxidation by the peroxygenase of Agrocybe aegerita

Three strategy rules of filamentous fungi in hydrocarbon remediation: an overview

Remediation of hydrocarbon contaminations requires much attention nowadays since it causes detrimental effects on land and even worse impacts on aquatic environments. Tools of bioremediation especially filamentous fungi permissible for cleaning up as much as conceivable, at least they turn into non-toxic residues with less consumed periods. Inorganic chemicals, CO2, H2O, and cell biomass are produced as a result of the breakdown and mineralization of petroleum hydrocarbon pollutants. This paper presents a detailed overview of three strategic rules of filamentous fungi in remediating the various aliphatic, and aromatic hydrocarbon compounds: utilizing carbons from hydrocarbons as sole energy, Co-metabolism manners (Enzymatic and Non-enzymatic theories), and Biosorption approaches. Upliftment in the degradation rate of complex hydrocarbon by the Filamentous Fungi in consortia scenario we can say, "Fungal Talk", which includes a variety of cellular mechanisms, including biosurfactant production, biomineralization, and precipitation, etc., This review not only displays its efficiency but showcases the field applications - cost-effective, reliable, eco-friendly, easy to culture as biomass, applicable in both land and any water bodies in operational environment cleanups. Nevertheless, the potentiality of fungi-human interaction has not been fully understood, henceforth further studies are highly endorsed with spore pathogenicity of the fungal species capable of high remediation rate, and the gene knockout study, if the specific peptides cause toxicity to any living matters via Genomics and Proteomics approaches, before application of any in situ or ex situ environments.

Soil processes modify the composition of volatile organic compounds (VOCs) from CO2- and CH4-dominated geogenic and landfill gases: A comprehensive study

Degradation mechanisms affecting non-methane volatile organic compounds (VOCs) during gas uprising from different hypogenic sources to the surface were investigated through extensive sampling surveys in areas encompassing a high enthalpy hydrothermal system associated with active volcanism, a CH4-rich sedimentary basin and a municipal waste landfill. For a comprehensive framework, published data from medium-to-high enthalpy hydrothermal systems were also included. The investigated systems were characterised by peculiar VOC suites that reflected the conditions of the genetic environments in which temperature, contents of organic matter, and gas fugacity had a major role. Differences in VOC patterns between source (gas vents and landfill gas) and soil gases indicated VOC transformations in soil. Processes acting in soil preferentially degraded high-molecular weight alkanes with respect to the low-molecular weight ones. Alkenes and cyclics roughly behaved like alkanes. Thiophenes were degraded to a larger extent with respect to alkylated benzenes, which were more reactive than benzene. Furan appeared less degraded than its alkylated homologues. Dimethylsulfoxide was generally favoured with respect to dimethylsulfide. Limonene and camphene were relatively unstable under aerobic conditions, while α-pinene was recalcitrant. O-bearing organic compounds (i.e., aldehydes, esters, ketones, alcohols, organic acids and phenol) acted as intermediate products of the ongoing VOC degradations in soil. No evidence for the degradation of halogenated compounds and benzothiazole was observed. This study pointed out how soil degradation processes reduce hypogenic VOC emissions and the important role played by physicochemical and biological parameters on the effective VOC attenuation capacity of the soil.

A ReaxFF Potential for Modeling Organic Matter Degradation with Oxybromine Oxidants

Oxidation of organic matter with oxybromine oxidants is ushering in a new era of enhanced hydrocarbon recovery. While these potent reagents are being tested in laboratory and field experiments, there is a pressing demand to delineate the molecular processes governing oxidation reactions at geological depth. Here, we parameterize a ReaxFF potential to model the oxidative decompositions of aliphatic and aromatic hydrocarbons in the presence of water-NaBr solutions that contain oxybromine (BrOn)- oxidizers. Our parameterization results in a reliable empirical bond-order potential that accurately calculates bond energies, exhibiting an RMSE of ∼1.18 eV, corresponding to 1.36 % average error. Reproducing bond dissociation and binding energies from Density Functional Theory (DFT), our parameterization proves transferable to aqueous environments. This H/C/O/Na/Br ReaxFF potential accurately reproduces the oxidation pathways of small hydrocarbons with oxybromine oxidizers. This force field captures proton and oxygen transfer, C-C bond tautomerization, and cleavage, leading to ring-opening and chain fragmentation. Molecular dynamic simulations demonstrate the oxidative degradation of aromatic and aliphatic kerogen-like moieties in bulk solutions. We envision that such reactive force fields will be useful to understand better the oxidation reactions of organic matter formed in geological reservoirs for enhanced shale gas recovery and improved carbon dioxide treatments.

DFT Mechanistic Investigation into Ni(II)-Catalyzed Hydroxylation of Benzene to Phenol by H2O2

Introduction of oxygen into aromatic C-H bonds is intriguing from both fundamental and practical perspectives. Although the 3d metal-catalyzed hydroxylation of arenes by H2O2 has been developed by several prominent researchers, a definitive mechanism for these crucial transformations remains elusive. Herein, density functional theory calculations were used to shed light on the mechanism of the established hydroxylation reaction of benzene with H2O2, catalyzed by [NiII(tepa)]2+ (tepa = tris[2-(pyridin-2-yl)ethyl]amine). Dinickel(III) bis(μ-oxo) species have been proposed as the key intermediate responsible for the benzene hydroxylation reaction. Our findings indicate that while the dinickel dioxygen species can be generated as a stable structure, it cannot serve as an active catalyst in this transformation. The calculations allowed us to unveil an unprecedented mechanism composed of six main steps as follows: (i) deprotonation of coordinated H2O2, (ii) oxidative addition, (iii) water elimination, (iv) benzene addition, (v) ketone generation, and (vi) tautomerization and regeneration of the active catalyst. Addition of benzene to oxygen, which occurs via a radical mechanism, turns out to be the rate-determining step in the overall reaction. This study demonstrates the critical role of Ni-oxyl species in such transformations, highlighting how the unpaired spin density value on oxygen and positive charges on the Ni-O• complex affect the activation barrier for benzene addition.

Machine Learning Approaches Identify Chemical Features for Stage-Specific Antimalarial Compounds

Efficacy data from diverse chemical libraries, screened against the various stages of the malaria parasite Plasmodium falciparum, including asexual blood stage (ABS) parasites and transmissible gametocytes, serve as a valuable reservoir of information on the chemical space of compounds that are either active (or not) against the parasite. We postulated that this data can be mined to define chemical features associated with the sole ABS activity and/or those that provide additional life cycle activity profiles like gametocytocidal activity. Additionally, this information could provide chemical features associated with inactive compounds, which could eliminate any future unnecessary screening of similar chemical analogs. Therefore, we aimed to use machine learning to identify the chemical space associated with stage-specific antimalarial activity. We collected data from various chemical libraries that were screened against the asexual (126 374 compounds) and sexual (gametocyte) stages of the parasite (93 941 compounds), calculated the compounds' molecular fingerprints, and trained machine learning models to recognize stage-specific active and inactive compounds. We were able to build several models that predict compound activity against ABS and dual activity against ABS and gametocytes, with Support Vector Machines (SVM) showing superior abilities with high recall (90 and 66%) and low false-positive predictions (15 and 1%). This allowed the identification of chemical features enriched in active and inactive populations, an important outcome that could be mined for essential chemical features to streamline hit-to-lead optimization strategies of antimalarial candidates. The predictive capabilities of the models held true in diverse chemical spaces, indicating that the ML models are therefore robust and can serve as a prioritization tool to drive and guide phenotypic screening and medicinal chemistry programs.

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.

Peroxide-Mediated Oxygenation of Organic Compounds by Fungal Peroxygenases

Unspecific peroxygenases (UPOs), whose sequences can be found in the genomes of thousands of filamentous fungi, many yeasts and certain fungus-like protists, are fascinating biocatalysts that transfer peroxide-borne oxygen (from H2O2 or R-OOH) with high efficiency to a wide range of organic substrates, including less or unactivated carbons and heteroatoms. A twice-proline-flanked cysteine (PCP motif) typically ligates the heme that forms the heart of the active site of UPOs and enables various types of relevant oxygenation reactions (hydroxylation, epoxidation, subsequent dealkylations, deacylation, or aromatization) together with less specific one-electron oxidations (e.g., phenoxy radical formation). In consequence, the substrate portfolio of a UPO enzyme always combines prototypical monooxygenase and peroxidase activities. Here, we briefly review nearly 20 years of peroxygenase research, considering basic mechanistic, molecular, phylogenetic, and biotechnological aspects.

Synthesis of Indigo-Dyes from Indole Derivatives by Unspecific Peroxygenases and Their Application for In-Situ Dyeing

Tyrian purple (also known as royal or imperial purple) is the oldest known commercial pigment and still one of the most expensive dyes, often associated with the wardrobes of clergy and royalty. It is a brominated derivative of indigo, a natural dye that has been used since 4000 BC. Moreover, just recently, the therapeutic value of indigoids for the treatment of several disorders was discovered. The manufacturing of indigo derivatives by the existing chemical routes has become increasingly uninteresting due to the use of aggressive reagents, expensive starting materials and high-energy costs. Thus, both dyestuff manufacturers and the pharmaceutical industry are interested in the development of gentle preparation methods of indigoids from simple precursors. Here, we describe a simple enzymatic method for the one-step synthesis of Tyrian purple and other indigo derivatives with fungal peroxygenases (UPO, EC 1.11.2.1). The reaction does not require complex co-substrates and works well in phosphate buffers with H2O2 (<0.1 wt%) and less than 5% (v/v) acetonitrile as co-solvent. We demonstrate the scaling up of the reaction to 10 Liters and established thereupon an environmentally friendly combined synthesis and in-situ dyeing process, further simplifying the manufacturing of vat-dyed fabrics. Eventually, we screened a number of halogen-substituted indoles in the search for novel indigo derivatives, which may be of interest for pharmaceutical and/or dyeing purposes.

Structural and biochemical studies enlighten the unspecific peroxygenase from Hypoxylon sp. EC38 as an efficient oxidative biocatalyst

Unspecific peroxygenases (UPO) are glycosylated fungal enzymes that can selectively oxidize C-H bonds. UPOs employ hydrogen peroxide as oxygen donor and reductant. With such an easy-to-handle co-substrate and without the need of a reducing agent, UPOs are emerging as convenient oxidative biocatalysts. Here, an unspecific peroxygenase from Hypoxylon sp. EC38 (HspUPO) was identified in an activity-based screen of six putative peroxygenase enzymes that were heterologously expressed in Pichia pastoris. The enzyme was found to tolerate selected organic solvents such as acetonitrile and acetone. HspUPO is a versatile catalyst performing various reactions, such as the oxidation of prim- and sec-alcohols, epoxidations and hydroxylations. Semi-preparative biotransformations were demonstrated for the non-enantioselective oxidation of racemic 1-phenylethanol rac -1b (TON = 13000), giving the product with 88% isolated yield, and the oxidation of indole 6a to give indigo 6b (TON = 2800) with 98% isolated yield. HspUPO features a compact and rigid three-dimensional conformation that wraps around the heme and defines a funnel-shaped tunnel that leads to the heme iron from the protein surface. The tunnel extends along a distance of about 12 Å with a fairly constant diameter in its innermost segment. Its surface comprises both hydrophobic and hydrophilic groups for dealing with small-to-medium size substrates of variable polarities. The structural investigation of several protein-ligand complexes revealed that the active site of HspUPO is accessible to molecules of varying bulkiness and polarity with minimal or no conformational changes, explaining the relatively broad substrate scope of the enzyme. With its convenient expression system, robust operational properties, relatively small size, well-defined structural features, and diverse reaction scope, HspUPO is an exploitable candidate for peroxygenase-based biocatalysis.

Biocatalytic Syntheses of Antiplatelet Metabolites of the Thienopyridines Clopidogrel and Prasugrel Using Fungal Peroxygenases

Antithrombotic thienopyridines, such as clopidogrel and prasugrel, are prodrugs that undergo a metabolic two-step bioactivation for their pharmacological efficacy. In the first step, a thiolactone is formed, which is then converted by cytochrome P450-dependent oxidation via sulfenic acids to the active thiol metabolites. These metabolites are the active compounds that inhibit the platelet P2Y₁₂ receptor and thereby prevent atherothrombotic events. Thus far, described biocatalytic and chemical synthesis approaches to obtain active thienopyridine metabolites are rather complex and suffer from low yields. In the present study, several unspecific peroxygenases (UPOs, EC 1.11.2.1) known to efficiently mimic P450 reactions in vitro—but requiring only hydroperoxide as oxidant—were tested for biocatalytic one-pot syntheses. In the course of the reaction optimization, various parameters such as pH and reductant, as well as organic solvent and amount were varied. The best results for the conversion of 1 mM thienopyridine were achieved using 2 U mL⁻¹ of a UPO from agaric fungus Marasmius rotula (MroUPO) in a phosphate-buffered system (pH 7) containing 5 mM ascorbate, 2 mM h⁻¹ H₂O₂ and 20% acetone. The preparation of the active metabolite of clopidogrel was successful via a two-step oxidation with an overall yield of 25%. In the case of prasugrel, a cascade of porcine liver esterase (PLE) and MroUPO was applied, resulting in a yield of 44%. The two metabolites were isolated with high purity, and their structures were confirmed by MS and MS² spectrometry as well as NMR spectroscopy. The findings broaden the scope of UPO applications again and demonstrate that they can be effectively used for the selective synthesis of metabolites and late-state diversification of organic molecules, circumventing complex multistage chemical syntheses and providing sufficient material for structural elucidation, reference material, or cellular assays.

Reactive force fields for modeling oxidative degradation of organic matter in geological formations

In an attempt to better explore organic matter reaction and properties, at depth, to oxidative fluid additives, we have developed a new ReaxFF potential to model and describe the oxidative decompositions of aliphatic and aromatic hydrocarbons in the presence of the oxychlorine ClO _n ^- oxidizers. By carefully adjusting the new H/C/O/Cl parameters, we show that the potential energies in both training and validation sets correlate well with calculated density functional theory (DFT) energies. Our parametrization yields a reliable empirical reactive force field with an RMS error of ∼1.57 eV, corresponding to a 1.70% average error. At this accuracy level, the reactive force field provides a reliable atomic-level picture of thermodynamically favorable reaction pathways governing oxidative degradation of H/C/O/Cl compounds. We demonstrate this capability by studying the structural degradation of small aromatic and aliphatic hydrocarbons in the presence of oxychlorine oxidizers in aqueous environments. We envision that such reactive force fields will be critical in understanding the oxidation processes of organic matter in geological reservoirs and the design of the next generation of reactive fluids for enhanced shale gas recovery and improved carbon dioxide adsorption and sequestration.

Advances in enzymatic oxyfunctionalization of aliphatic compounds

Selective oxyfunctionalizations of aliphatic compounds are difficult chemical reactions, where enzymes can play an important role due to their stereo- and regio-selectivity and operation under mild reaction conditions. P450 monooxygenases are well-known biocatalysts that mediate oxyfunctionalization reactions in different living organisms (from bacteria to humans). Unspecific peroxygenases (UPOs), discovered in fungi, have arisen as "dream biocatalysts" of great biotechnological interest because they catalyze the oxyfunctionalization of aliphatic and aromatic compounds, avoiding the necessity of expensive cofactors and regeneration systems, and only depending on H₂O₂ for their catalysis. Here, we summarize recent advances in aliphatic oxyfunctionalization reactions by UPOs, as well as the molecular determinants of the enzyme structures responsible for their activities, emphasizing the differences found between well-known P450s and the novel fungal peroxygenases.

Dioxygen reactivity of iron(ii)–gentisate/1,4-dihydroxy-2-naphthoate complexes of N4 ligands: oxidative coupling of 1,4-dihydroxy-2-naphthoate

Oxidative C–C coupling of iron-coordinated co-ligand: Iron(ii)-1,4-dihydroxy-2-naphthoate complexes of neutral N4 ligands react with dioxygen to display C–C coupling of 1,4-dihydroxy-2-naphthoate.

A hydroquinone-specific screening system for directed P450 evolution

The direct hydroxylation of benzene to hydroquinone (HQ) under mild reaction conditions is a challenging task for chemical catalysts. Cytochrome P450 (CYP) monooxygenases are known to catalyze the oxidation of a variety of aromatic compounds with atmospheric dioxygen. Protein engineering campaigns led to the identification of novel P450 variants, which yielded improvements in respect to activity, specificity, and stability. An effective screening strategy is crucial for the identification of improved enzymes with desired characteristics in large mutant libraries. Here, we report a first screening system designed for screening of P450 variants capable to produce hydroquinones. The hydroquinone quantification assay is based on the interaction of 4-nitrophenylacetonitrile (NpCN) with hydroquinones under alkaline conditions. In the 96-well plate format, a low detection limit (5 μM) and a broad linear detection range (5 to 250 μM) were obtained. The NpCN assay can be used for the quantification of dihydroxylated aromatic compounds such as hydroquinones, catechols, and benzoquinones. We chose the hydroxylation of pseudocumene by P450 BM3 as a target reaction and screened for improved trimethylhydroquinone (TMHQ) formation. The new P450 BM3 variant AW2 (R47Q, Y51F, I401M, A330P) was identified by screening a saturation mutagenesis library of amino acid position A330 with the NpCN assay. In summary, a 70-fold improved TMHQ formation was achieved with P450 BM3 AW2 when compared to the wild type (WT) and a 1.8-fold improved TMHQ formation compared to the recently reported P450 BM3 M3 (R47S, Y51W, A330F, I401M).

An Enzymatic Route to α-Tocopherol Synthons: Aromatic Hydroxylation of Pseudocumene and Mesitylene with P450 BM3

Aromatic hydroxylation of pseudocumene (1 a) and mesitylene (1 b) with P450 BM3 yields key phenolic building blocks for α-tocopherol synthesis. The P450 BM3 wild-type (WT) catalyzed selective aromatic hydroxylation of 1 b (94 %), whereas 1 a was hydroxylated to a large extent on benzylic positions (46-64 %). Site-saturation mutagenesis generated a new P450 BM3 mutant, herein named "variant M3" (R47S, Y51W, A330F, I401M), with significantly increased coupling efficiency (3- to 8-fold) and activity (75- to 230-fold) for the conversion of 1 a and 1 b. Additional π-π interactions introduced by mutation A330F improved not only productivity and coupling efficiency, but also selectivity toward aromatic hydroxylation of 1 a (61 to 75 %). Under continuous nicotinamide adenine dinucleotide phosphate recycling, the novel P450 BM3 variant M3 was able to produce the key tocopherol precursor trimethylhydroquinone (3 a; 35 % selectivity; 0.18 mg mL^-1 ) directly from 1 a. In the case of 1 b, overoxidation leads to dearomatization and the formation of a valuable p-quinol synthon that can directly serve as an educt for the synthesis of 3 a. Detailed product pattern analysis, substrate docking, and mechanistic considerations support the hypothesis that 1 a binds in an inverted orientation in the active site of P450 BM3 WT, relative to P450 BM3 variant M3, to allow this change in chemoselectivity. This study provides an enzymatic route to key phenolic synthons for α-tocopherols and the first catalytic and mechanistic insights into direct aromatic hydroxylation and dearomatization of trimethylbenzenes with O₂ .

Fungal Unspecific Peroxygenases Oxidize the Majority of Organic EPA Priority Pollutants

Unspecific peroxygenases (UPOs) are secreted fungal enzymes with promiscuity for oxygen transfer and oxidation reactions. Functionally, they represent hybrids of P450 monooxygenases and heme peroxidases; phylogenetically they belong to the family of heme-thiolate peroxidases. Two UPOs from the basidiomycetous fungi Agrocybe aegerita (AaeUPO) and Marasmius rotula (MroUPO) converted 35 out of 40 compounds listed as EPA priority pollutants, including chlorinated benzenes and their derivatives, halogenated biphenyl ethers, nitroaromatic compounds, polycyclic aromatic hydrocarbons (PAHs) and phthalic acid derivatives. These oxygenations and oxidations resulted in diverse products and—if at all—were limited for three reasons: (i) steric hindrance caused by multiple substitutions or bulkiness of the compound as such (e.g., hexachlorobenzene or large PAHs), (ii) strong inactivation of aromatic rings (e.g., nitrobenzene), and (iii) low water solubility (e.g., complex arenes). The general outcome of our study is that UPOs can be considered as extracellular counterparts of intracellular monooxygenases, both with respect to catalyzed reactions and catalytic versatility. Therefore, they should be taken into consideration as a relevant biocatalytic detoxification and biodegradation tool used by fungi when confronted with toxins, xenobiotics and pollutants in their natural environments.

Mechanisms on the Impacts of Alkalinity, pH, and Chloride on Persulfate-Based Groundwater Remediation

Persulfate (S₂O₈^2-)-based in situ chemical oxidation (ISCO) has gained more attention in recent years due to the generation of highly reactive and selective sulfate radical (SO₄^•-). This study examined the effects of important groundwater chemical parameters, i.e., alkalinity, pH, and chloride on benzene degradation via heterogeneous persulfate activation by three Fe(III)- and Mn(IV)-containing aquifer minerals: ferrihydrite, goethite, and pyrolusite. A comprehensive kinetic model was established to elucidate the mechanisms of radical generation and mineral surface complexation. Results showed that an increase of alkalinity up to 10 meq/L decreased the rates of persulfate decomposition and benzene degradation, which was associated with the formation of unreactive surface carbonato complexes. An increase in pH generally accelerated persulfate decomposition due to enhanced formation of reactive surface hydroxo complexation. A change in the chloride level up to 5 mM had a negligibly effect on the reaction kinetics. Kinetics modeling also suggested that SO₄^•- was transformed to hydroxyl radical (HO^•) and carbonate radical (CO₃^•-) at higher pHs. Furthermore, the yields of two major products of benzene oxidation, i.e., phenol and aldehyde, were positively correlated with the branching ratio of SO₄^•- reacting with benzene, but inversely correlated with that of HO^• or CO₃^•-, indicating that SO₄^•- preferentially oxidized benzene via pathways involving fewer hydroxylation steps compared to HO^• or CO₃^•-.

Will 1,2-dihydro-1,2-azaborine-based drugs resist metabolism by cytochrome P450 compound I?

1,2-dihydro-1,2-azaborine is a structural and electronic analogue of benzene which is able to occupy benzene-binding pockets in T4 lysozyme and has been proposed as suitable arene-mimicking group for biological and pharmaceutical applications. Its applicability in a biological context requires it to be able to resist modification by xenobiotic-degrading enzymes like the P450 cytochromes. Quantum chemical computations described in this work show that 1,2-dihydro-1,2-azaborine is much more prone to modification by these enzymes than benzene, unless steric crowding of the ring prevents it from reaching the active site, or otherwise only allows reaction at the less reactive C₄-position. This novel heterocyclic compound is therefore expected to be of limited usefulness as an aryl bioisostere.

Molecular determinants for selective C25-hydroxylation of vitamins D2and D3by fungal peroxygenases

Regioselective hydroxylation of vitamin D byAgrocybe aegeritaandCoprinopsis cinereaperoxygenases was investigated in an experimental and computational study.

Synthetic biosensors for precise gene control and real-time monitoring of metabolites

Characterization and standardization of inducible transcriptional regulators has transformed how scientists approach biology by allowing precise and tunable control of gene expression. Despite their utility, only a handful of well-characterized regulators exist, limiting the complexity of engineered biological systems. We apply a characterization pipeline to four genetically encoded sensors that respond to acrylate, glucarate, erythromycin and naringenin. We evaluate how the concentration of the inducing chemical relates to protein expression, how the extent of induction affects protein expression kinetics, and how the activation behavior of single cells relates to ensemble measurements. We show that activation of each sensor is orthogonal to the other sensors, and to other common inducible systems. We demonstrate independent control of three fluorescent proteins in a single cell, chemically defining eight unique transcriptional states. To demonstrate biosensor utility in metabolic engineering, we apply the glucarate biosensor to monitor product formation in a heterologous glucarate biosynthesis pathway and identify superior enzyme variants. Doubling the number of well-characterized inducible systems makes more complex synthetic biological circuits accessible. Characterizing sensors that transduce the intracellular concentration of valuable metabolites into fluorescent readouts enables high-throughput screening of biological catalysts and alleviates the primary bottleneck of the metabolic engineering design-build-test cycle.

Directed evolution of unspecific peroxygenase from Agrocybe aegerita

Unspecific peroxygenase (UPO) represents a new type of heme-thiolate enzyme with self-sufficient mono(per)oxygenase activity and many potential applications in organic synthesis. With a view to taking advantage of these properties, we subjected the Agrocybe aegerita UPO1-encoding gene to directed evolution in Saccharomyces cerevisiae. To promote functional expression, several different signal peptides were fused to the mature protein, and the resulting products were tested. Over 9,000 clones were screened using an ad hoc dual-colorimetric assay that assessed both peroxidative and oxygen transfer activities. After 5 generations of directed evolution combined with hybrid approaches, 9 mutations were introduced that resulted in a 3,250-fold total activity improvement with no alteration in protein stability. A breakdown between secretion and catalytic activity was performed by replacing the native signal peptide of the original parental type with that of the evolved mutant; the evolved leader increased functional expression 27-fold, whereas an 18-fold improvement in the kcat/Km value for oxygen transfer activity was obtained. The evolved UPO1 was active and highly stable in the presence of organic cosolvents. Mutations in the hydrophobic core of the signal peptide contributed to enhance functional expression up to 8 mg/liter, while catalytic efficiencies for peroxidative and oxygen transfer reactions were increased by several mutations in the vicinity of the heme access channel. Overall, the directed-evolution platform described is a valuable point of departure for the development of customized UPOs with improved features and for the study of structure-function relationships.

Oxidations catalyzed by fungal peroxygenases

The enzymatic oxyfunctionalization of organic molecules under physiological conditions has attracted keen interest from the chemical community. Unspecific peroxygenases (EC 1.11.2.1) secreted by fungi represent an intriguing enzyme type that selectively transfers peroxide-borne oxygen with high efficiency to diverse substrates including unactivated hydrocarbons. They are glycosylated heme-thiolate enzymes that form a separate superfamily of heme proteins. Among the catalyzed reactions are hydroxylations, epoxidations, dealkylations, oxidations of organic hetero atoms and inorganic halides as well as one-electron oxidations. The substrate spectrum of fungal peroxygenases and the product patterns show similarities both to cytochrome P450 monooxygenases and classic heme peroxidases. Given that selective oxyfunctionalizations are among the most difficult to realize chemical reactions and that respectively transformed molecules are of general importance in organic and pharmaceutical syntheses, it will be worth developing peroxygenase biocatalysts for industrial applications.