4-hydroxyacetophenone Monooxygenase Research Articles

Key genes of electron transfer, the nitrogen cycle and tetracycline removal in bioelectrochemical systems

BackgroundSoil microbial fuel cells (MFCs) can remove antibiotics and antibiotic resistance genes (ARGs) simultaneously, but their removal mechanism is unclear. In this study, metagenomic analysis was employed to reveal the functional genes involved in degradation, electron transfer and the nitrogen cycle in the soil MFC.ResultsThe results showed that the soil MFC effectively removed tetracycline in the overlapping area of the cathode and anode, which was 64% higher than that of the control. The ARGs abundance increased by 14% after tetracycline was added (54% of the amplified ARGs belonged to efflux pump genes), while the abundance decreased by 17% in the soil MFC. Five potential degraders of tetracycline were identified, especially the species Phenylobacterium zucineum, which could secrete the 4-hydroxyacetophenone monooxygenase encoded by EC 1.14.13.84 to catalyse deacylation or decarboxylation. Bacillus, Geobacter, Anaerolinea, Gemmatirosa kalamazoonesis and Steroidobacter denitrificans since ubiquinone reductase (encoded by EC 1.6.5.3), succinate dehydrogenase (EC 1.3.5.1), Coenzyme Q-cytochrome c reductase (EC 1.10.2.2), cytochrome-c oxidase (EC 1.9.3.1) and electron transfer flavoprotein-ubiquinone oxidoreductase (EC 1.5.5.1) served as complexes I, II, III, IV and ubiquinone, respectively, to accelerate electron transfer. Additionally, nitrogen metabolism-related gene abundance increased by 16% to support the microbial efficacy in the soil MFC, and especially EC 1.7.5.1, and coding the mutual conversion between nitrite and nitrate was obviously improved.ConclusionsThe soil MFC promoted functional bacterial growth, increased functional gene abundance (including nitrogen cycling, electron transfer, and biodegradation), and facilitated antibiotic and ARG removal. Therefore, soil MFCs have expansive prospects in the remediation of antibiotic-contaminated soil. This study provides insight into the biodegradation mechanism at the gene level in soil bioelectrochemical remediation.

Microbial community structure and exploration of bioremediation enzymes: functional metagenomics insight into Arabian Sea sediments

Deep-sea sediments provide important information on oceanic biogeochemical processes mediated by the microbiome and their functional roles which could be unravelled using genomic tools. The present study aimed to delineate microbial taxonomic and functional profiles from Arabian Sea sediment samples through whole metagenome sequencing using Nanopore technology. Arabian Sea is considered as a major microbial reservoir with significant bio-prospecting potential which needs to be explored extensively using recent advances in genomics. Assembly, co-assembly, and binning methods were used to predict Metagenome Assembled Genomes (MAGs) which were further characterized by their completeness and heterogeneity. Nanopore sequencing of Arabian Sea sediment samples generated around 1.73 tera basepairs of data. Proteobacteria (78.32%) was found to be the most dominant phylum followed by Bacteroidetes (9.55%) and Actinobacteria (2.14%) in the sediment metagenome. Further, 35 MAGs from assembled and 38 MAGs of co-assembled reads were generated from long-read sequence dataset with major representations from the genera Marinobacter, Kangiella, and Porticoccus. RemeDB analysis revealed a high representation of pollutant-degrading enzymes involved in hydrocarbon, plastic and dye degradation. Validation of enzymes with long nanopore reads using BlastX resulted in better characterization of complete gene signatures involved in hydrocarbon (6-monooxygenase and 4-hydroxyacetophenone monooxygenase) and dye degradation (Arylsulfatase). Enhancing the cultivability of deep-sea microbes predicted from the uncultured WGS approaches by I-tip method resulted in isolation of facultative extremophiles. This study presents a comprehensive insight into the taxonomic and functional profiles of Arabian Sea sediments, indicating a potential hotspot for bioprospection.

A novel 4-hydroxyacetophenone monooxygenase featuring aromatic substrates preference for enantioselective access to sulfoxides

Baeyer-Villiger monooxygenases are recognized as valuable tools for biooxidative synthesis of chiral sulfoxides. In this work, a novel HAPMO ortholog from Pseudomonas fluorescens (HAPMOPf) was identified by genome mining. Evolutionary relationship and sequence analysis revealed that HAPMOPf belongs to the family of typical type I BVMOs. HAPMOPf has a low KM value (0.025 mM) toward 4-hydroxyacetophenone, and a half-life of 24 h at 30 °C and pH 9.0. HAPMOPf exhibited distinct activity toward aromatic ketones as well as various thioethers, such as methyl phenyl sulfide and bromo‑methyl phenyl sulfide. The highest activities of HAPMOPf was 1.47 U·mg−1 toward 4-hydroxyacetophenone among tested ketone and thioether substrates. Furthermore, over 95% enantioselectivity was determined toward methyl phenyl sulfides with ortho, meta, and para-substituents (Cl, Br, CHO, NH2). Therefore, HAPMOPf is a promising biocatalyst for the synthesis of aromatic esters and chiral sulfoxides.

Functional divergence between closely related Baeyer-Villiger monooxygenases from Aspergillus flavus

• Four new fungal Baeyer-Villiger monooxygenases cloned and characterized. • Phylogenetic subgroup diverged from CPMO-type BVMOs. • Paralogues showing different substrate scope and specificity. • Kinetic resolution of rac -bicyclo[3.2.0]hept-2-en-6-one. Baeyer-Villiger monooxygenases (BVMOs) catalyse the chemo-, regio- and enantioselective oxidation of ketones to esters and lactones. To date, most of the cloned BVMOs available are derived from bacteria, although Baeyer-Villiger oxidations using fungi have frequently been demonstrated. Here we report the cloning and characterization of four BVMOs from the fungus Aspergillus flavus NRRL3357. Phylogenetic analysis shows these four BVMOs to cluster in a distinct group apart from other well-characterized BVMOs including cyclohexanone, phenylacetone and 4-hydroxyacetophenone monooxygenase. Building on the Grogan classification/clustering of BVMOs, we have designated this new group of BVMOs, Group VI. Group VI BVMOs show an early divergence from the cyclopentanone monooxygenase (CPMO) type BVMOs (Group I). Substrate profiling using cyclic, bicyclic, aliphatic and aryl ketones show a clear divergence in function and specificity not only between this new group of BVMOs and the CPMO-type BVMOs, but also between the four A. flavus BVMO paralogues despite their high sequence similarity. This study not only contributes to the growing number of available BVMOs, but also addresses the current classification of Type I BVMOs, and the usefulness of phylogenetic clustering and prediction of function and selectivity when genome-mining is used to search for new biocatalysts.

A high-throughput assay method to quantify Baeyer–Villiger monooxygenase activity

An assay for the spectrophotometric determination of Baeyer–Villiger monooxygenase (BVMO) activity is described. Baeyer–Villiger oxidation of p-nitroacetophenone generates the corresponding acetate and subsequent hydrolysis of this ester by an esterase or NaOH results in the formation of p-nitrophenolate. This chromophore can be easily quantified spectrophotometrically at 410 nm. The assay can be performed in a microtiter plate format and is applicable to whole Escherichia coli cells containing recombinant BVMO, crude cell extract as well as using purified enzyme as exemplified for the 4-hydroxyacetophenone monooxygenase (HAPMO) from Pseudomonas putida JD1. Furthermore, the assay was used to identify more active HAPMO variants within enzyme mutant libraries generated by error-prone PCR or site-saturation mutagenesis.

Scale-up of Baeyer–Villiger monooxygenase-catalyzed synthesis of enantiopure compounds

Several Baeyer-Villiger monooxygenases converting a wide spectrum of substrates have been discovered, cloned, and characterized throughout the last few years. Still, only a few of them are applicable for large-scale conversion predominantly due to their sensitivity towards high substrate and/or product concentrations. The recently cloned and characterized 4-hydroxyacetophenone monooxygenase from Pseudomonas putida JD1 shows excellent enantioselectivity towards 3-phenyl-2-butanone with E > 100 but is inhibited by concentrations >10 mM of both substrate and product. This obstacle could be circumvented by in situ substrate feed and product removal using a hydrophobic Lewatit® adsorbent resin. Thus, the concentration of 3-phenyl-2-butanone could be increased from 1.4 to >26 mM without significant reduction in conversion.

BVMO-catalysed dynamic kinetic resolution of racemic benzyl ketones in the presence of anion exchange resins

4-Hydroxyacetophenone monooxygenase from Pseudomonas fluorescens ACB was employed in the presence of a weak anion exchange resin to perform dynamic kinetic resolutions of racemic benzyl ketones with high conversions and good optical purities. Different parameters that affect to the efficiency of the enzymatic Baeyer-Villiger oxidation and racemisation were analyzed in order to optimize the activity and selectivity of the biocatalytic system.

Cloning, expression, characterization, and biocatalytic investigation of the 4-hydroxyacetophenone monooxygenase from Pseudomonas putida JD1.

While the number of available recombinant Baeyer-Villiger monooxygenases (BVMOs) has grown significantly over the last few years, there is still the demand for other BVMOs to expand the biocatalytic diversity. Most BVMOs that have been described are dedicated to convert efficiently cyclohexanone and related cyclic aliphatic ketones. To cover a broader range of substrate types and enantio- and/or regioselectivities, new BVMOs have to be discovered. The gene encoding a BVMO identified in Pseudomonas putida JD1 converting aromatic ketones (HAPMO; 4-hydroxyacetophenone monooxygenase) was amplified from genomic DNA using SiteFinding-PCR, cloned, and functionally expressed in Escherichia coli. Furthermore, four other open reading frames could be identified clustered around this HAPMO. It has been suggested that these proteins, including the HAPMO, might be involved in the degradation of 4-hydroxyacetophenone. Substrate specificity studies revealed that a large variety of other arylaliphatic ketones are also converted via Baeyer-Villiger oxidation into the corresponding esters, with preferences for para-substitutions at the aromatic ring. In addition, oxidation of aldehydes and some heteroaromatic compounds was observed. Cycloketones and open-chain ketones were not or poorly accepted, respectively. It was also found that this enzyme oxidizes aromatic ketones such as 3-phenyl-2-butanone with excellent enantioselectivity (E >>100).

Elucidation of the 4-Hydroxyacetophenone Catabolic Pathway in Pseudomonas fluorescens ACB

The catabolism of 4-hydroxyacetophenone in Pseudomonas fluorescens ACB is known to proceed through the intermediate formation of hydroquinone. Here, we provide evidence that hydroquinone is further degraded through 4-hydroxymuconic semialdehyde and maleylacetate to beta-ketoadipate. The P. fluorescens ACB genes involved in 4-hydroxyacetophenone utilization were cloned and characterized. Sequence analysis of a 15-kb DNA fragment showed the presence of 14 open reading frames containing a gene cluster (hapCDEFGHIBA) of which at least four encoded enzymes are involved in 4-hydroxyacetophenone degradation: 4-hydroxyacetophenone monooxygenase (hapA), 4-hydroxyphenyl acetate hydrolase (hapB), 4-hydroxymuconic semialdehyde dehydrogenase (hapE), and maleylacetate reductase (hapF). In between hapF and hapB, three genes encoding a putative intradiol dioxygenase (hapG), a protein of the Yci1 family (hapH), and a [2Fe-2S] ferredoxin (hapI) were found. Downstream of the hap genes, five open reading frames are situated encoding three putative regulatory proteins (orf10, orf12, and orf13) and two proteins possibly involved in a membrane efflux pump (orf11 and orf14). Upstream of hapE, two genes (hapC and hapD) were present that showed weak similarity with several iron(II)-dependent extradiol dioxygenases. Based on these findings and additional biochemical evidence, it is proposed that the hapC and hapD gene products are involved in the ring cleavage of hydroquinone.

Enzymatic kinetic resolution of racemic ketones catalyzed by Baeyer–Villiger monooxygenases

A set of racemic cyclic and linear ketones, as well as 2-phenylpropionaldehyde, were tested as substrates in the enzymatic Baeyer–Villiger oxidation catalyzed by two Baeyer–Villiger monooxygenases: phenylacetone monooxygenase (PAMO) and 4-hydroxyacetophenone monooxygenase (HAPMO). Excellent enantioselectivites ( E > 200) can be obtained in the kinetic resolution processes depending on the substrate structure and the reaction conditions. The parameters affecting the biocatalytic properties of these enzymes were also studied, in order to establish a deeper understanding of these novel biocatalysts.

Biocatalytic properties of Baeyer–Villiger monooxygenases in aqueous–organic media

The biocatalytic properties of three Baeyer–Villiger monooxygenases (phenylacetone monooxygenase, 4-hydroxyacetophenone monooxygenase and ethionamide monooxygenase) in a variety of aqueous–organic media were studied using organic sulfides as substrates. The influence of the nature and the concentration of the solvents, as well as of the substrates, on the activity and enantioselectivity of the enzymes was investigated in detail. Solvents were found to decrease, to a different extent, enzyme activity. High increases of enantioselectivity and also reversal of enantiopreference were observed depending on the enzyme and on the nature of the solvent and the substrate employed.

4-Hydroxyacetophenone monooxygenase from Pseudomonas fluorescens ACB as an oxidative biocatalyst in the synthesis of optically active sulfoxides

Recombinant 4-hydroxyacetophenone monooxygenase (HAPMO) from Pseudomonas fluorescens ACB has been tested as a catalyst in sulfoxidation reactions on a set of aromatic sulfides. With a few exceptions, excellent enantioselectivities in the synthesis of chiral phenyl and benzyl sulfoxides were achieved. The bacterial Baeyer–Villiger monooxygenase was also shown to accept racemic sulfoxides, a prochiral diketone and an organoboron compound as substrates. This study demonstrates the great biocatalytic potential of this novel oxidative enzyme.

Coenzyme Binding during Catalysis Is Beneficial for the Stability of 4-Hydroxyacetophenone Monooxygenase

The NADPH-dependent dimeric flavoenzyme 4-hydroxyacetophenone monooxygenase (HAPMO) catalyzes Baeyer-Villiger oxidations of a wide range of ketones, thereby generating esters or lactones. In the current work, we probed HAPMO-coenzyme complexes present during the enzyme catalytic cycle with the aim to gain mechanistic insight. Moreover, we investigated the structural role of the nicotinamide coenzyme. For these studies, we used (i) wild type HAPMO, (ii) the R339A variant, which is active but has a low affinity toward NADPH, and (iii) the R440A variant, which is inactive but has a high affinity toward NADPH. Electrospray ionization mass spectrometry was used as the primary tool to directly observe noncovalent protein-coenzyme complexes in real time. These analyzes showed for the first time that the nicotinamide coenzyme remains bound to HAPMO during the entire catalytic cycle of the NADPH oxidase reaction. This may also have implications for other homologous Baeyer-Villiger monooxygenases. Together with the observations that NADP(+) only weakly interacts with oxidized enzyme and that HAPMO is mainly in the reduced form during catalysis, we concluded that NADP(+) interacts tightly with the reduced form of HAPMO. We also demonstrated that the association with the coenzyme is crucial for enzyme stability. The interaction with the coenzyme analog 3-aminopyridine adenine dinucleotide phosphate (AADP(+)) strongly enhanced the thermal stability of wild type HAPMO. This coenzyme-induced stabilization may also be important for related enzymes.

Biooxidation of ketones with a cyclobutanone structural motif by recombinant whole-cells expressing 4-hydroxyacetophenone monooxygenase

Whole cells of an Escherichia coli strain overexpressing 4-hydroxyacetophenone monooxygenase (HAPMO) originating from Pseudomonas fluorescens ACB have been used to study the stereopreference in the Baeyer–Villiger reaction of ketones bearing a cyclobutanone structural motif. The enzyme catalyzes the oxidation of several prochiral cyclobutanones to antipodal butyrolactones as obtained in cyclohexanone monooxygenase mediated conversions. However, chemical yields and enantiomeric purity are usually moderate. The regioselectivity in oxidations of fused cylobutanones differs from the previously observed behavior for Baeyer–Villiger monooxygenases with highly varying ratios of “normal” and “abnormal” product lactones and enantioselectivities. Taken together with previous substrate profiling data, HAPMO represents a distinctively different biocatalytic entity compared to monooxygenases characterized so far.

Identifying determinants of NADPH specificity in Baeyer–Villiger monooxygenases

The Baeyer-Villiger monooxygenase (BVMO), 4-hydroxyacetophenone monooxygenase (HAPMO), uses NADPH and O(2) to oxidize a variety of aromatic ketones and sulfides. The FAD-containing enzyme has a 700-fold preference for NADPH over NADH. Sequence alignment with other BVMOs, which are all known to be selective for NADPH, revealed three conserved basic residues, which could account for the observed coenzyme specificity. The corresponding residues in HAPMO (Arg339, Lys439 and Arg440) were mutated and the properties of the purified mutant enzymes were studied. For Arg440 no involvement in coenzyme recognition could be shown as mutant R440A was totally inactive. Although this mutant could still be fully reduced by NADPH, no oxygenation occurred, indicating that this residue is crucial for completing the catalytic cycle of HAPMO. Characterization of several Arg339 and Lys439 mutants revealed that these residues are indeed both involved in coenzyme recognition. Mutant R339A showed a largely decreased affinity for NADPH, as judged from kinetic analysis and binding experiments. Replacing Arg339 also resulted in a decreased catalytic efficiency with NADH. Mutant K439A displayed a 100-fold decrease in catalytic efficiency with NADPH, mainly caused by an increased K(m). However, the efficiency with NADH increased fourfold. Saturation mutagenesis at position 439 showed that the presence of an asparagine or a phenylalanine improves the catalytic efficiency with NADH by a factor of 6 to 7. All Lys439 mutants displayed a lower affinity for AADP(+), confirming a role of the lysine in recognizing the 2'-phosphate of NADPH. The results obtained could be extrapolated to the sequence-related cyclohexanone monooxygenase. Replacing Lys326 in this BVMO, which is analogous to Lys439 in HAPMO, again changed the coenzyme specificity towards NADH. These results indicate that the strict NADPH dependency of this class of monooxygenases is based upon recognition of the coenzyme by several basic residues.

Flavoenzyme‐Catalyzed Oxygenations and Oxidations of Phenolic Compounds

AbstractFor Abstract see ChemInform Abstract in Full Text.

Substrate Specificity and Enantioselectivity of 4-Hydroxyacetophenone Monooxygenase

The 4-hydroxyacetophenone monooxygenase (HAPMO) from Pseudomonas fluorescens ACB catalyzes NADPH- and oxygen-dependent Baeyer-Villiger oxidation of 4-hydroxyacetophenone to the corresponding acetate ester. Using the purified enzyme from recombinant Escherichia coli, we found that a broad range of carbonylic compounds that are structurally more or less similar to 4-hydroxyacetophenone are also substrates for this flavin-containing monooxygenase. On the other hand, several carbonyl compounds that are substrates for other Baeyer-Villiger monooxygenases (BVMOs) are not converted by HAPMO. In addition to performing Baeyer-Villiger reactions with aromatic ketones and aldehydes, the enzyme was also able to catalyze sulfoxidation reactions by using aromatic sulfides. Furthermore, several heterocyclic and aliphatic carbonyl compounds were also readily converted by this BVMO. To probe the enantioselectivity of HAPMO, the conversion of bicyclohept-2-en-6-one and two aryl alkyl sulfides was studied. The monooxygenase preferably converted (1R,5S)-bicyclohept-2-en-6-one, with an enantiomeric ratio (E) of 20, thus enabling kinetic resolution to obtain the (1S,5R) enantiomer. Complete conversion of both enantiomers resulted in the accumulation of two regioisomeric lactones with moderate enantiomeric excess (ee) for the two lactones obtained [77% ee for (1S,5R)-2 and 34% ee for (1R,5S)-3]. Using methyl 4-tolyl sulfide and methylphenyl sulfide, we found that HAPMO is efficient and highly selective in the asymmetric formation of the corresponding (S)-sulfoxides (ee > 99%). The biocatalytic properties of HAPMO described here show the potential of this enzyme for biotechnological applications.

Flavoenzyme-Catalyzed Oxygenations and Oxidations of Phenolic Compounds

Flavin-dependent monooxygenases and oxidases play an important role in the mineralization of phenolic compounds. Because of their exquisite regioselectivity and stereoselectivity, these enzymes are of interest for the biocatalytic production of fine chemicals and food ingredients. In our group, we have characterized several flavoenzymes that act on phenolic compounds, including 4-hydroxybenzoate 3-hydroxylase, 3-hydroxyphenylacetate 6-hydroxylase, 4-hydroxybenzoate 1-hydroxylase (decarboxylating), hydroquinone hydroxylase, 2-hydroxybiphenyl 3-monooxygenase, phenol hydroxylase, 4-hydroxyacetophenone monooxygenase and vanillyl-alcohol oxidase. The catalytic properties of these enzymes are reviewed here, together with insights obtained from site-directed and random mutagenesis.

Identification of a Baeyer–Villiger monooxygenase sequence motif

Baeyer–Villiger monooxygenases (BVMOs) form a distinct class of flavoproteins that catalyze the insertion of an oxygen atom in a C–C bond using dioxygen and NAD(P)H. Using newly characterized BVMO sequences, we have uncovered a BVMO-identifying sequence motif: FXGXXXHXXXW(P/D). Studies with site-directed mutants of 4-hydroxyacetophenone monooxygenase from Pseudomonas fluorescens ACB suggest that this fingerprint sequence is critically involved in catalysis. Further sequence analysis showed that the BVMOs belong to a novel superfamily that comprises three known classes of FAD-dependent monooxygenases: the so-called flavin-containing monooxygenases (FMOs), the N-hydroxylating monooxygenases (NMOs), and the BVMOs. Interestingly, FMOs contain an almost identical sequence motif when compared to the BVMO sequences: FXGXXXHXXX(Y/F). Using these novel amino acid sequence fingerprints, BVMOs and FMOs can be readily identified in the protein sequence databank.

4-Hydroxyacetophenone monooxygenase from Pseudomonas fluorescens ACB. A novel flavoprotein catalyzing Baeyer-Villiger oxidation of aromatic compounds.

A novel flavoprotein that catalyses the NADPH-dependent oxidation of 4-hydroxyacetophenone to 4-hydroxyphenyl acetate, was purified to homogeneity from Pseudomonas fluorescens ACB. Characterization of the purified enzyme showed that 4-hydroxyacetophenone monooxygenase (HAPMO) is a homodimer of approximately 140 kDa with each subunit containing a noncovalently bound FAD molecule. HAPMO displays a tight coupling between NADPH oxidation and substrate oxygenation. Besides 4-hydroxyacetophenone a wide range of other acetophenones are readily converted via a Baeyer-Villiger rearrangement reaction into the corresponding phenyl acetates. The P. fluorescens HAPMO gene (hapE) was characterized. It encoded a 640 amino-acid protein with a deduced mass of 71 884 Da. Except for an N-terminal extension of approximately 135 residues, the sequence of HAPMO shares significant similarity with two known types of Baeyer-Villiger monooxygenases: cyclohexanone monooxygenase (27-33% sequence identity) and steroid monooxygenase (33% sequence identity). The HAPMO sequence contains several sequence motifs indicative for the presence of two Rossman fold domains involved in FAD and NADPH binding. The functional role of a recently identified flavoprotein sequence motif (ATG) was explored by site-directed mutagenesis. Replacement of the strictly conserved glycine (G490) resulted in a dramatic effect on catalysis. From a kinetic analysis of the G490A mutant it is concluded that the observed sequence motif serves a structural function which is of importance for NADPH binding.