Purification and Characterization of a 1,4-Benzoquinone Reductase from the Basidiomycete Phanerochaete chrysosporium

Biotransformation of the azo dye reactive orange 16 by Aspergillus flavus A5P1: Performance, genetic background, pathway, and mechanism

This study reports the strain Aspergillus flavus A5P1 (A5P1), which is with the capable of degrading the azo dye reactive orange 16 (RO16). The mechanism of RO16 degradation by A5P1 was elucidated through genomic analysis, enzymatic analysis, degradation pathway analysis and oxidative stress analysis. Strain A5P1 exhibited aerobic degradation of RO16, with optimal degradation at an initial pH of 3.0. Genomic analysis indicates that strain A5P1 possesses the potential for acid tolerance and degradation of azo dye. Enzymatic analysis, combined with degradation product analysis, demonstrated that extracellular laccase, intracellular lignin peroxidase, and intracellular quinone reductase were likely key enzymes in the RO16 degradation process. Oxidative stress analysis revealed that cell stress responses may participate in the RO16 biotransformation process. The results indicated that the biotransformation of RO16 may involves biological processes such as transmembrane transport of RO16, cometabolism of the strain with RO16, and cell stress responses. These findings shed light on the biodegradation of RO16 by A5P1, indicating A5P1's potential for environmental remediation.

Role of quinone reductases in extracellular redox cycling in lichenized ascomycetes

Our previous work showed that many lichenized Ascomycetes can generate hydroxyl radicals using quinone-based extracellular redox cycling. During cycling, hydroquinones must be formed and subsequently regenerated from quinones using a quinone reductase (QR). However, we also showed that no simple correlation exists between QR activity and rates of hydroxyl radical formation. To further investigate the role of QR in hydroxyl radical formation, three model lichen species, Leptogium furfuraceum, Lasallia pustulata and Peltigera membranacea were selected for further investigation. All possessed QR activity and could metabolize quinones, and both Leptogium furfuraceum and Lasallia pustulata actively produced hydroxyl radicals. By contrast, P. membranacea produced almost no hydroxyl radicals, and although the lichen readily metabolized quinones, no hydroquinone production was detected. Peltigera had laccase (LAC) activity that was c. 50 times higher than in the other two species, suggesting that LAC rapidly oxidizes the hydroquinones, preventing radical formation deriving from auto-oxidation. It appears that in some lichens hydroxyl radical formation is blocked by the presence of high redox enzyme activity. QR from P. didactyla was studied further and found to display similar properties to the enzyme from free-living fungi, although it possessed an unusually high molecular mass (c. 62 kDa).

A Putative Lignin Copper Oxidase from Trichoderma reesei

The ability of Trichoderma reesei, a fungus widely used for the commercial production of hemicellulases and cellulases, to grow and modify technical soda lignin was investigated. By quantifying fungal genomic DNA, T. reesei showed growth and sporulation in solid and liquid cultures containing lignin alone. The analysis of released soluble lignin and residual insoluble lignin was indicative of enzymatic oxidative conversion of phenolic lignin side chains and the modification of lignin structure by cleaving the β-O-4 linkages. The results also showed that polymerization reactions were taking place. A proteomic analysis conducted to investigate secreted proteins at days 3, 7, and 14 of growth revealed the presence of five auxiliary activity (AA) enzymes in the secretome: AA6, AA9, two AA3 enzymes), and the only copper radical oxidase encoded in the genome of T. reesei. This enzyme was heterologously produced and characterized, and its activity on lignin-derived molecules was investigated. Phylogenetic characterization demonstrated that this enzyme belonged to the AA5_1 family, which includes characterized glyoxal oxidases. However, the enzyme displayed overlapping physicochemical and catalytic properties across the AA5 family. The enzyme was remarkably stable at high pH and oxidized both, alcohols and aldehydes with preference to the alcohol group. It was also active on lignin-derived phenolic molecules as well as simple carbohydrates. HPSEC and LC-MS analyses on the reactions of the produced protein on lignin dimers (SS ββ, SS βO4 and GG β5) uncovered the polymerizing activity of this enzyme, which was accordingly named lignin copper oxidase (TrLOx). Polymers of up 10 units were formed by hydroxy group oxidation and radical formation. The activations of lignin molecules by TrLOx along with the co-secretion of this enzyme with reductases and FAD flavoproteins oxidoreductases during growth on lignin suggest a synergistic mechanism for lignin breakdown.

Differential Roles of a Family of Flavodoxin-Like Proteins That Promote Resistance to Quinone-Mediated Oxidative Stress in Candida albicans

Survival of the fungal pathogen Candida albicans within a mammalian host relies on its ability to resist oxidative stress. The four flavodoxin-like proteins (Pst1, Pst2, Pst3, and Ycp4) that reside on the inner surface of the C. albicans plasma membrane represent a recently discovered antioxidant mechanism that is essential for virulence. Flavodoxin-like proteins combat oxidative stress by promoting a two-electron reduction of quinone molecules, which prevents the formation of toxic semiquinone radicals. Previous studies indicated that Pst3 played a major role in promoting resistance to the small quinone molecules p-benzoquinone and menadione. Analysis of additional quinones confirmed this role for Pst3. To better define their function, antibodies were raised against each of the four flavodoxin-like proteins and used to quantify protein levels. Interestingly, the basal level of flavodoxin-like proteins differed, with Pst3 and Ycp4 being the most abundant. However, after induction with p-benzoquinone, Pst1 and Pst3 were the most highly induced, resulting in Pst3 becoming the most abundant. Constitutive expression of the flavodoxin-like protein genes from a TDH3 promoter resulted in similar protein levels and showed that Pst1 and Pst3 were better at protecting C. albicans against p-benzoquinone than Pst2 or Ycp4. In contrast, Pst1 and Ycp4 provided better protection against oxidative damage induced by tert-butyl hydroperoxide. Thus, both the functional properties and the relative abundance contribute to the distinct roles of the flavodoxin-like proteins in resisting oxidative stress. These results further define how C. albicans combats the host immune response and survives in an environment rich in oxidative stress.

Biodegradation and Kinetic Analysis of Acetaminophen with Co-culture of Bacterial Strains Isolated from Sewage Wastewater

Acetaminophen (paracetamol, APAP) is one of the fastest growing pharmaceutical pollutants in the environment and has been classified under among the emerging organic pollutants (EOPs). The increasing concentration of it in our environment is not only harmful to the ecosystem, but also to the humans as well. In this study, the microscopy, biochemical test and 16S rRNA sequencing the characterization of APAP as the sole degrading stains viz. Staphylococcus sciuri strain DPP1 (MN744326), Bacillus subtilis strain DPP3 (MN744327), Bacillus paralicheniformis strain DKP1 (MN744324), Enterococcus faecium strain DKP2 (MN744325) and DDP2 (MT705211) were performed. Haldane's growth kinetic model was used to identify specific growth rate and observed for DPP1 (485 mg/L), DPP3 (593 mg/L), DKP1 (477 mg/L), DKP2 (702 mg/L) and DDP2 (685 mg/L). The maximum specific growth rate was reported for the stains viz. DPP1, DPP3, DKP1, DKP2, and DDP2, was in order of 0.076, 0.223, 0.259, 0.179, and 0.141, respectively. The Box-Behnken Design (BBD) was used to identify the effect of physical parameters on degradation using mathematical modeling. The analysis of variance (ANOVA) showed that the strains DPP1, DPP3, DKP1, DKP2, and DDP2 had significant F-value and regression coefficient (R²) value of 0.01%, 0.06%, 0.37%, and 0.18%, respectively. The co-culture of the five strains has utilized 1200 mg/L of APAP within 70 h while individual strains took 10 days. The intermediate metabolites like 4-aminophenol, benzamide, (R)-2-methylpentanoic acid, methylene-3-vinyl cyclohexane, and 1,5-hexadiene were identified by GC-MS. The degradation metabolic pathway was predicted by the intermediates by GC-MS, and PathPred based analysis.

Flavodoxin-Like Proteins Protect Candida albicans from Oxidative Stress and Promote Virulence

The fungal pathogen Candida albicans causes lethal systemic infections in humans. To better define how pathogens resist oxidative attack by the immune system, we examined a family of four Flavodoxin-Like Proteins (FLPs) in C. albicans. In agreement with previous studies showing that FLPs in bacteria and plants act as NAD(P)H quinone oxidoreductases, a C. albicans quadruple mutant lacking all four FLPs (pst1Δ, pst2Δ, pst3Δ, ycp4Δ) was more sensitive to benzoquinone. Interestingly, the quadruple mutant was also more sensitive to a variety of oxidants. Quinone reductase activity confers important antioxidant effects because resistance to oxidation was restored in the quadruple mutant by expressing either Escherichia coli wrbA or mammalian NQO1, two distinct types of quinone reductases. FLPs were detected at the plasma membrane in C. albicans, and the quadruple mutant was more sensitive to linolenic acid, a polyunsaturated fatty acid that can auto-oxidize and promote lipid peroxidation. These observations suggested that FLPs reduce ubiquinone (coenzyme Q), enabling it to serve as an antioxidant in the membrane. In support of this, a C. albicans coq3Δ mutant that fails to synthesize ubiquinone was also highly sensitive to oxidative stress. FLPs are critical for survival in the host, as the quadruple mutant was avirulent in a mouse model of systemic candidiasis under conditions where infection with wild type C. albicans was lethal. The quadruple mutant cells initially grew well in kidneys, the major site of C. albicans growth in mice, but then declined after the influx of neutrophils and by day 4 post-infection 33% of the mice cleared the infection. Thus, FLPs and ubiquinone are important new antioxidant mechanisms that are critical for fungal virulence. The potential of FLPs as novel targets for antifungal therapy is further underscored by their absence in mammalian cells.

Tenebrionid secretions and a fungal benzoquinone oxidoreductase form competing components of an arms race between a host and pathogen

Entomopathogenic fungi and their insect hosts represent a model system for examining invertebrate-pathogen coevolutionary selection processes. Here we report the characterization of competing components of an arms race consisting of insect protective antimicrobial compounds and evolving fungal mechanisms of detoxification. The insect pathogenic fungus Beauveria bassiana has a remarkably wide host range; however, some insects are resistant to fungal infection. Among resistant insects is the tenebrionid beetle Tribolium castaneum that produces benzoquinone-containing defensive secretions. Reduced fungal germination and growth was seen in media containing T. castaneum dichloromethane extracts or synthetic benzoquinone. In response to benzoquinone exposure, the fungus expresses a 1,4-benzoquinone oxidoreductase, BbbqrA, induced >40-fold. Gene knockout mutants (ΔBbbqrA) showed increased growth inhibition, whereas B. bassiana overexpressing BbbqrA (Bb::BbbqrA(O)) displayed increased resistance to benzoquinone compared with wild type. Increased benzoquinone reductase activity was detected in wild-type cells exposed to benzoquinone and in the overexpression strain. Heterologous expression and purification of BbBqrA in Escherichia coli confirmed NAD(P)H-dependent benzoquinone reductase activity. The ΔBbbqrA strain showed decreased virulence toward T. castaneum, whereas overexpression of BbbqrA increased mortality versus T. castaneum. No change in virulence was seen for the ΔBbbqrA or Bb::BbbqrA(O) strains when tested against the greater wax moth Galleria mellonella or the beetle Sitophilus oryzae, neither of which produce significant amounts of cuticular quinones. The observation that artificial overexpression of BbbqrA results in increased virulence only toward quinone-secreting insects implies the lack of strong selection or current failure of B. bassiana to counteradapt to this particular host defense throughout evolution.

Direct fungal fermentation of lignocellulosic biomass into itaconic, fumaric, and malic acids: current and future prospects

Various economic and environmental sustainability concerns as well as consumer preference for bio-based products from natural sources have paved the way for the development and expansion of biorefining technologies. These involve the conversion of renewable biomass feedstock to fuels and chemicals using biological systems as alternatives to petroleum-based products. Filamentous fungi possess an expansive portfolio of products including the multifunctional organic acids itaconic, fumaric, and malic acids that have wide-ranging current applications and potentially addressable markets as platform chemicals. However, current bioprocessing technologies for the production of these compounds are mostly based on submerged fermentation, which necessitates physicochemical pretreatment and hydrolysis of lignocellulose biomass to soluble fermentable sugars in liquid media. This review will focus on current research work on fungal production of itaconic, fumaric, and malic acids and perspectives on the potential application of solid-state fungal cultivation techniques for the consolidated hydrolysis and organic acid fermentation of lignocellulosic biomass.

Genes involved in degradation of para-nitrophenol are differentially arranged in form of non-contiguous gene clusters in Burkholderia sp. strain SJ98

Biodegradation of para-Nitrophenol (PNP) proceeds via two distinct pathways, having 1,2,3-benzenetriol (BT) and hydroquinone (HQ) as their respective terminal aromatic intermediates. Genes involved in these pathways have already been studied in different PNP degrading bacteria. Burkholderia sp. strain SJ98 degrades PNP via both the pathways. Earlier, we have sequenced and analyzed a ~41 kb fragment from the genomic library of strain SJ98. This DNA fragment was found to harbor all the lower pathway genes; however, genes responsible for the initial transformation of PNP could not be identified within this fragment. Now, we have sequenced and annotated the whole genome of strain SJ98 and found two ORFs (viz., pnpA and pnpB) showing maximum identity at amino acid level with p-nitrophenol 4-monooxygenase (PnpM) and p-benzoquinone reductase (BqR). Unlike the other PNP gene clusters reported earlier in different bacteria, these two ORFs in SJ98 genome are physically separated from the other genes of PNP degradation pathway. In order to ascertain the identity of ORFs pnpA and pnpB, we have performed in-vitro assays using recombinant proteins heterologously expressed and purified to homogeneity. Purified PnpA was found to be a functional PnpM and transformed PNP into benzoquinone (BQ), while PnpB was found to be a functional BqR which catalyzed the transformation of BQ into hydroquinone (HQ). Noticeably, PnpM from strain SJ98 could also transform a number of PNP analogues. Based on the above observations, we propose that the genes for PNP degradation in strain SJ98 are arranged differentially in form of non-contiguous gene clusters. This is the first report for such arrangement for gene clusters involved in PNP degradation. Therefore, we propose that PNP degradation in strain SJ98 could be an important model system for further studies on differential evolution of PNP degradation functions.

Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes

BACKGROUND

Since its inception, the carbohydrate-active enzymes database (CAZy; http://www.cazy.org) has described the families of enzymes that cleave or build complex carbohydrates, namely the glycoside hydrolases (GH), the polysaccharide lyases (PL), the carbohydrate esterases (CE), the glycosyltransferases (GT) and their appended non-catalytic carbohydrate-binding modules (CBM). The recent discovery that members of families CBM33 and family GH61 are in fact lytic polysaccharide monooxygenases (LPMO), demands a reclassification of these families into a suitable category.

RESULTS

Because lignin is invariably found together with polysaccharides in the plant cell wall and because lignin fragments are likely to act in concert with (LPMO), we have decided to join the families of lignin degradation enzymes to the LPMO families and launch a new CAZy class that we name "Auxiliary Activities" in order to accommodate a range of enzyme mechanisms and substrates related to lignocellulose conversion. Comparative analyses of these auxiliary activities in 41 fungal genomes reveal a pertinent division of several fungal groups and subgroups combining their phylogenetic origin and their nutritional mode (white vs. brown rot).

CONCLUSIONS

The new class introduced in the CAZy database extends the traditional CAZy families, and provides a better coverage of the full extent of the lignocellulose breakdown machinery.

Cloning, expression and purification of cindoxin, an unusual Fmn-containing cytochrome p450 redox partner

Cytochromes P450 (P450s) belong to a superfamily of haemoproteins that catalyse a remarkable variety of oxidative transformations. P450 catalysis generally requires that cognate redox proteins transfer electrons, derived ultimately from NAD(P)H, to the P450 for oxygen activation. P450(cin) (CYP176A1) is a bacterial P450 that is postulated to allow Citrobacter braakii to live on cineole as its sole carbon source by initiating cineole biodegradation. Here we report the cloning, expression, purification and characterisation of one of its postulated redox partners, cindoxin (Cdx), which has strong similarity to the FMN domain of cytochrome P450 reductase. Cindoxin reductase (CdR), which displays strong similarity to NADPH-dependent ferredoxin reductases, was unable to be expressed in a functional form. Mass spectrometric and HPLC analyses confirmed that the flavin cofactor of cindoxin was FMN. Redox potentiometric titrations were performed with cindoxin within the range 6<pH<8; this enabled the quinone/semiquinone (E(1)) and semiquinone/hydroquinone (E(2)) redox potentials to be determined. Our results show that cindoxin might be somewhat different to other flavodoxins that interact with P450s, in which generally only one couple is important. Both redox states of cindoxin could be catalytically relevant. A catalytically active system was reconstituted in vitro with E. coli flavodoxin reductase (Fpr) acting as the terminal redox partner in the absence of CdR. Our results show that Cdx and Fpr support regio- and stereoselective P450(cin)-catalysed cineole oxidation to (1R)-6beta-hydroxycineole with turnover rates up to 1500 min(-1). This system is tightly coupled with 80 % of NADPH reducing equivalents funnelled into substrate oxidation.

Fungal biodegradation and enzymatic modification of lignin

Lignin, the most abundant aromatic biopolymer on Earth, is extremely recalcitrant to degradation. By linking to both hemicellulose and cellulose, it creates a barrier to any solutions or enzymes and prevents the penetration of lignocellulolytic enzymes into the interior lignocellulosic structure. Some basidiomycetes white-rot fungi are able to degrade lignin efficiently using a combination of extracellular ligninolytic enzymes, organic acids, mediators and accessory enzymes. This review describes ligninolytic enzyme families produced by these fungi that are involved in wood decay processes, their molecular structures, biochemical properties and the mechanisms of action which render them attractive candidates in biotechnological applications. These enzymes include phenol oxidase (laccase) and heme peroxidases [lignin peroxidase (LiP), manganese peroxidase (MnP) and versatile peroxidase (VP)]. Accessory enzymes such as H(2)O(2)-generating oxidases and degradation mechanisms of plant cell-wall components in a non-enzymatic manner by production of free hydroxyl radicals (·OH) are also discussed.

Proteomic analysis ofTrichoderma atroviridemycelia stressed by organophosphate pesticide dichlorvos

The proteomic approach is a powerful tool to study microbial response to environmental stress. To evaluate the responses of Trichoderma spp. to the organophosphate pesticide dichlorvos, mycelia of Trichoderma atroviride T23 were exposed to dichlorvos at concentrations of 0, 100, 300, 500, and 1000 µg/mL, respectively. Changes in protein expression were investigated using two-dimensional sodium dodecyl sulfate – polyacrylamide gel electrophoresis. Sixteen protein spots were differentially expressed. They were identified by MALDI–TOF/TOF MS and were found to be linked to energy metabolism, transport, signal transduction, and stress tolerance. Among stress-related proteins, glutathione peroxidase-like protein (GPX), 1,4-benzoquinone reductase, and HEX1 were upregulated by and cyclophilin A induced by 1000 µg/mL dichlorvos when compared with the control. These proteins were considered to be associated with fungal adaptation to adverse conditions. The results will help us to understand molecular mechanisms through which Trichoderma responds to organophosphate pesticides.

Pyranose dehydrogenases: biochemical features and perspectives of technological applications

Pyranose dehydrogenase is a fungal flavin-dependent sugar oxidoreductase which is structurally and catalytically related to fungal pyranose oxidase and cellobiose dehydrogenase and probably fulfills similar biological functions in lignocellulose breakdown. It is a monomeric secretory glycoprotein and is limited to a rather small group of litter-decomposing basidiomycetes. Compared with pyranose oxidase, it displays broader substrate specificity and a variable regioselectivity and is unable to utilize oxygen as electron acceptor using substituted benzoquinones and (organo) metallic ions instead. Depending on the structure of the sugar in pyranose form (mono/di/oligosaccharide or glycoside) and the enzyme source, selective monooxidations at C-1, C-2, C-3, or dioxidations at C-2,3 or C-3,4 of the molecule to the corresponding aldonolactones (C-1), or (di)dehydrosugars (aldos(di)uloses) can be performed. These features make pyranose dehydrogenase a promising and versatile biocatalyst for production of highly reactive, sometimes unique, di- and tri-carbonyl sugar derivatives that may serve as interesting chiral intermediates for the synthesis of rare sugars, novel drugs, and fine chemicals.

Fungal bioconversion of lignocellulosic residues; opportunities & perspectives

The development of alternative energy technology is critically important because of the rising prices of crude oil, security issues regarding the oil supply, and environmental issues such as global warming and air pollution. Bioconversion of biomass has significant advantages over other alternative energy strategies because biomass is the most abundant and also the most renewable biomaterial on our planet. Bioconversion of lignocellulosic residues is initiated primarily by microorganisms such as fungi and bacteria which are capable of degrading lignocellulolytic materials. Fungi such as Trichoderma reesei and Aspergillus niger produce large amounts of extracellular cellulolytic enzymes, whereas bacterial and a few anaerobic fungal strains mostly produce cellulolytic enzymes in a complex called cellulosome, which is associated with the cell wall. In filamentous fungi, cellulolytic enzymes including endoglucanases, cellobiohydrolases (exoglucanases) and beta-glucosidases work efficiently on cellulolytic residues in a synergistic manner. In addition to cellulolytic/hemicellulolytic activities, higher fungi such as basidiomycetes (e.g. Phanerochaete chrysosporium) have unique oxidative systems which together with ligninolytic enzymes are responsible for lignocellulose degradation. This review gives an overview of different fungal lignocellulolytic enzymatic systems including extracellular and cellulosome-associated in aerobic and anaerobic fungi, respectively. In addition, oxidative lignocellulose-degradation mechanisms of higher fungi are discussed. Moreover, this paper reviews the current status of the technology for bioconversion of biomass by fungi, with focus on mutagenesis, co-culturing and heterologous gene expression attempts to improve fungal lignocellulolytic activities to create robust fungal strains.

Induction of extracellular hydroxyl radical production by white-rot fungi through quinone redox cycling

A simple strategy for the induction of extracellular hydroxyl radical (OH) production by white-rot fungi is presented. It involves the incubation of mycelium with quinones and Fe(3+)-EDTA. Succinctly, it is based on the establishment of a quinone redox cycle catalyzed by cell-bound dehydrogenase activities and the ligninolytic enzymes (laccase and peroxidases). The semiquinone intermediate produced by the ligninolytic enzymes drives OH production by a Fenton reaction (H(2)O(2) + Fe(2+) --> OH + OH(-) + Fe(3+)). H(2)O(2) production, Fe(3+) reduction, and OH generation were initially demonstrated with two Pleurotus eryngii mycelia (one producing laccase and versatile peroxidase and the other producing just laccase) and four quinones, 1,4-benzoquinone (BQ), 2-methoxy-1,4-benzoquinone (MBQ), 2,6-dimethoxy-1,4-benzoquinone (DBQ), and 2-methyl-1,4-naphthoquinone (menadione [MD]). In all cases, OH radicals were linearly produced, with the highest rate obtained with MD, followed by DBQ, MBQ, and BQ. These rates correlated with both H(2)O(2) levels and Fe(3+) reduction rates observed with the four quinones. Between the two P. eryngii mycelia used, the best results were obtained with the one producing only laccase, showing higher OH production rates with added purified enzyme. The strategy was then validated in Bjerkandera adusta, Phanerochaete chrysosporium, Phlebia radiata, Pycnoporus cinnabarinus, and Trametes versicolor, also showing good correlation between OH production rates and the kinds and levels of the ligninolytic enzymes expressed by these fungi. We propose this strategy as a useful tool to study the effects of OH radicals on lignin and organopollutant degradation, as well as to improve the bioremediation potential of white-rot fungi.

Pyranose 2-oxidase from Phanerochaete chrysosporium--expression in E. coli and biochemical characterization

The presented work reports the isolation and heterologous expression of the p2ox gene encoding the flavoprotein pyranose 2-oxidase (P2Ox) from the basidiomycete Phanerochaete chrysosporium. The p2ox cDNA was inserted into the bacterial expression vector pET21a(+) and successfully expressed in Escherichia coli. We obtained active, fully flavinylated recombinant P2Ox in yields of approximately 270 mg/l medium. The recombinant enzyme was provided with an N-terminal T7-tag and a C-terminal His(6)-tag to facilitate simple one-step purification. We obtained an apparently homogenous enzyme preparation with a specific activity of 16.5 U/mg. Recombinant P2Ox from P. chrysosporium was characterized in some detail with respect to its physical and catalytic properties, both for electron donor (sugar substrates) and - for the first time - alternative electron acceptors (1,4-benzoquinone, substituted quinones, 2,6-dichloroindophenol and ferricenium ion). As judged from the catalytic efficiencies k(cat)/K(m), some of these alternative electron acceptors are better substrates than oxygen, which might have implications for the proposed in vivo function of pyranose 2-oxidase.

Cotton benzoquinone reductase: up-regulation during early fiber development and heterologous expression and characterization in Pichia pastoris

Benzoquinone reductase (BR; EC 1.6.5.7) is an enzyme which catalyzes the bivalent redox reactions of quinones without the production of free radical intermediates. Using 2D-PAGE comparisons, two proteins were found to be up-regulated in wild-type cotton ovules during the fiber initiation stage but not in the fiberless line SL 1-7-1. These proteins were excised from the gel, partially sequenced and identified to be BR isoforms. PCR was used to amplify both full length coding regions of 609bp and once cloned, the restriction enzyme HindIII was used to distinguish the clones encoding the BR1 (one site) and BR2 (two sites) isoforms. Both deduced protein sequences had 203 residues which differed at 14 residues. The molecular mass and pIs were similar between the measured protein (2D-PAGE) and the theoretical protein (deduced). Heterologous proteins BR1 and BR2 were produced for further study by ligating the BR1 and BR2 clones in frame into the alpha-factor secretion sequence in pPICZalphaA vector and expressed with Pichia pastoris. Both BR1 and BR2 were approximately 26.5kDa and did enzymatically reduce 2,6-dimethoxybenzoquinone similar to the fungal BR.

Crystal structure of the NADH:quinone oxidoreductase WrbA from Escherichia coli

The flavoprotein WrbA, originally described as a tryptophan (W) repressor-binding protein in Escherichia coli, has recently been shown to exhibit the enzymatic activity of a NADH:quinone oxidoreductase. This finding points toward a possible role in stress response and in the maintenance of a supply of reduced quinone. We have determined the three-dimensional structure of the WrbA holoprotein from E. coli at high resolution (1.66 A), and we observed a characteristic, tetrameric quaternary structure highly similar to the one found in the WrbA homologs of Deinococcus radiodurans and Pseudomonas aeruginosa. A similar tetramer was originally observed in an iron-sulfur flavoprotein involved in the reduction of reactive oxygen species. Together with other, recently characterized proteins such as YhdA or YLR011wp (Lot6p), these tetrameric flavoproteins may constitute a large family with diverse functions in redox catalysis. WrbA binds substrates at an active site that provides an ideal stacking environment for aromatic moieties, while providing a pocket that is structured to stabilize the ADP part of an NADH molecule in its immediate vicinity. Structures of WrbA in complex with benzoquinone and NADH suggest a sequential binding mechanism for both molecules in the catalytic cycle.

WrbA from Escherichia coli and Archaeoglobus fulgidus is an NAD(P)H:quinone oxidoreductase

WrbA (tryptophan [W] repressor-binding protein) was discovered in Escherichia coli, where it was proposed to play a role in regulation of the tryptophan operon; however, this has been put in question, leaving the function unknown. Here we report a phylogenetic analysis of 30 sequences which indicated that WrbA is the prototype of a distinct family of flavoproteins which exists in a diversity of cell types across all three domains of life and includes documented NAD(P)H:quinone oxidoreductases (NQOs) from the Fungi and Viridiplantae kingdoms. Biochemical characterization of the prototypic WrbA protein from E. coli and WrbA from Archaeoglobus fulgidus, a hyperthermophilic species from the Archaea domain, shows that these enzymes have NQO activity, suggesting that this activity is a defining characteristic of the WrbA family that we designate a new type of NQO (type IV). For E. coli WrbA, the K(m)(NADH) was 14 +/- 0.43 microM and the K(m)(benzoquinone) was 5.8 +/- 0.12 microM. For A. fulgidus WrbA, the K(m)(NADH) was 19 +/- 1.7 microM and the K(m)(benzoquinone) was 37 +/- 3.6 microM. Both enzymes were found to be homodimeric by gel filtration chromatography and homotetrameric by dynamic light scattering and to contain one flavin mononucleotide molecule per monomer. The NQO activity of each enzyme is retained over a broad pH range, and apparent initial velocities indicate that maximal activities are comparable to the optimum growth temperature for the respective organisms. The results are discussed and implicate WrbA in the two-electron reduction of quinones, protecting against oxidative stress.

An NADH:quinone oxidoreductase active during biodegradation by the brown-rot basidiomycete Gloeophyllum trabeum

The brown-rot basidiomycete Gloeophyllum trabeum uses a quinone redox cycle to generate extracellular Fenton reagent, a key component of the biodegradative system expressed by this highly destructive wood decay fungus. The hitherto uncharacterized quinone reductase that drives this cycle is a potential target for inhibitors of wood decay. We have identified the major quinone reductase expressed by G. trabeum under conditions that elicit high levels of quinone redox cycling. The enzyme comprises two identical 22-kDa subunits, each with one molecule of flavin mononucleotide. It is specific for NADH as the reductant and uses the quinones produced by G. trabeum (2,5-dimethoxy-1,4-benzoquinone and 4,5-dimethoxy-1,2-benzoquinone) as electron acceptors. The affinity of the reductase for these quinones is so high that precise kinetic parameters were not obtainable, but it is clear that k(cat)/K(m) for the quinones is greater than 10(8) M(-1) s(-1). The reductase is encoded by a gene with substantial similarity to NAD(P)H:quinone reductase genes from other fungi. The G. trabeum quinone reductase may function in quinone detoxification, a role often proposed for these enzymes, but we hypothesize that the fungus has recruited it to drive extracellular oxyradical production.

FQR1, a novel primary auxin-response gene, encodes a flavin mononucleotide-binding quinone reductase

FQR1 is a novel primary auxin-response gene that codes for a flavin mononucleotide-binding flavodoxin-like quinone reductase. Accumulation of FQR1 mRNA begins within 10 min of indole-3-acetic acid application and reaches a maximum of approximately 10-fold induction 30 min after treatment. This increase in FQR1 mRNA abundance is not diminished by the protein synthesis inhibitor cycloheximide, demonstrating that FQR1 is a primary auxin-response gene. Sequence analysis reveals that FQR1 belongs to a family of flavin mononucleotide-binding quinone reductases. Partially purified His-tagged FQR1 isolated from Escherichia coli catalyzes the transfer of electrons from NADH and NADPH to several substrates and exhibits in vitro quinone reductase activity. Overexpression of FQR1 in plants leads to increased levels of FQR1 protein and quinone reductase activity, indicating that FQR1 functions as a quinone reductase in vivo. In mammalian systems, glutathione S-transferases and quinone reductases are classified as phase II detoxification enzymes. We hypothesize that the auxin-inducible glutathione S-transferases and quinone reductases found in plants also act as detoxification enzymes, possibly to protect against auxin-induced oxidative stress.

Purification and characterization of pyranose oxidase from the white rot fungus Trametes multicolor

We purified an intracellular pyranose oxidase from mycelial extracts of the white rot fungus Trametes multicolor by using ammonium sulfate fractionation, hydrophobic interaction, ion-exchange chromatography, and gel filtration. The native enzyme has a molecular mass of 270 kDa as determined by equilibrium ultracentrifugation and is composed of four identical 68-kDa subunits as determined by matrix-assisted laser desorption ionization mass spectrometry. Each subunit contains one covalently bound flavin adenine dinucleotide as its prosthetic group. The enzyme oxidizes several aldopyranoses specifically at position C-2, and its preferred electron donor substrates are D-glucose, D-xylose, and L-sorbose. During this oxidation reaction electrons are transferred to oxygen, yielding hydrogen peroxide. In addition, the enzyme catalyzes the two-electron reduction of 1,4-benzoquinone, several substituted benzoquinones, and 2,6-dichloroindophenol, as well as the one-electron reduction of the ABTS [2,2'-azinobis(3-ethylbenzthiazolinesulfonic acid)] cation radical. As judged by the catalytic efficiencies (k(cat)/K(m)), some of these quinone electron acceptors are much better substrates for pyranose oxidase than oxygen. The optimum pH of the pyranose oxidase-catalyzed reaction depends strongly on the electron acceptor employed and varies from 4 to 8. It has been proposed that the main metabolic function of pyranose oxidase is as a constituent of the ligninolytic system of white rot fungi that provides peroxidases with H(2)O(2). An additional function could be reduction of quinones, key intermediates that are formed during mineralization of lignin.

Quinone oxidoreductase message levels are differentially regulated in parasitic and non-parasitic plants exposed to allelopathic quinones

Allelopathic chemicals released by plants into the rhizosphere have effects on neighboring plants ranging from phytoxicity to inducing organogenesis. The allelopathic activity of naturally occurring quinones and phenols is primarily a function of reactive radicals generated during redox cycling between quinone and hydroquinone states. We isolated cDNAs encoding two distinct quinone oxidoreductases from roots of the parasitic plant Triphysaria treated with the allelopathic quinone 2,6-dimethoxybenzoquinone (DMBQ). TvQR1 is a member of the zeta-crystallin quinone oxidoreductase family that catalyzes one-electron quinone reductions, generating free radical semiquinones. TvQR2 belongs to a family of detoxifying quinone oxidoreductases that catalyze bivalent redox reactions which avoid the radical intermediate. TvQR1 and TvQR2 message levels are rapidly upregulated in Triphysaria roots as a primary response to treatment with various allelopathic quinones. Inhibition of quinone oxidoreductase enzymatic activity with dicumarol prior to quinone treatment resulted in increased transcript levels. While TvQR2 homologs were upregulated by DMBQ in roots of all plants examined, TvQR1 homologs were upregulated only in roots of parasitic plants. Phylogenetic trees constructed of TvQR1 and TvQR2 protein homologs in Archea, Eubacteria and Eukaryotes indicated that both gene families are ancient, yet the families have dissimilar evolutionary histories in angiosperms. We hypothesize that TvQR2-like proteins function to detoxify allelopathic quinones in the rhizosphere, while TvQR1 has specific functions associated with haustorium development in parasitic plants.

Peroxidative degradation of selected PCB: a mechanistic study

The enzyme-induced decomposition and biodegradation of PCB were investigated. 2,5-Dichlorobiphenyl (PCB 9) and 2,2',5,5'-tetrachlorobiphenyl (PCB 52) were used as example compounds to study efficiency and mechanism of the degradation processes. It was found that the application of horseradish peroxidase (HRP) together with defined amounts of hydrogen peroxide removed 90%, of the initial concentration of PCB 9 and 55% of the initial concentration of PCB 52 from an aqueous solution after a reaction period of 220 min. Dechlorination was observed as the initial step. Although the metabolites identified were mainly chlorinated hydroxybiphenyls, benzoic acids and non-substituted 1,1'-biphenyl, some higher chlorinated biphenyl isomers also appeared. The biodegradation of PCB 9 using the white rot fungus Trametes multicolor took about four weeks and reduction was about 80%, of the initial concentration. The metabolites produced (dichlorobenzenes, chlorophenols and alkylated benzenes) were not quite the same as those observed upon incubation with HRP.

Cloning and heterologous expression of NAD(P)H:quinone reductase of Arabidopsis thaliana, a functional homologue of animal DT-diaphorase

In higher plants, NAD(P)H:quinone reductase (NQR) is the only flavoreductase known to reduce quinone substrates directly to hydroquinones by a two-electron reaction mechanism. This enzymatic activity is believed to protect aerobic organisms from the oxidative action of semiquinones. For this reason plant NQR has recently been suggested to be related to animal DT-diaphorase. A cDNA clone for NQR of Arabidopsis thaliana was identified, expressed in Escherichia coli, purified and characterized. Its amino acid sequence was found related to a number of putative proteins, mostly from prokaryotes, with still undetermined function. Conversely, in spite of the functional homology, sequence similarity between plant NQR and animal DT-diaphorase was limited and essentially confined to the flavin binding site.

De novo synthesis of 4,5-dimethoxycatechol and 2, 5-dimethoxyhydroquinone by the brown rot fungus Gloeophyllum trabeum

The new dimethoxycatechol 4,5-dimethoxy-1,2-benzenediol (DMC) and the new dimethoxyhydroquinone 2,5-dimethoxy-1,4-benzenediol (DMH) were isolated from stationary cultures of the brown rot fungus Gloeophyllum trabeum growing on a glucose mineral medium protected from light. The structure was elucidated by gas chromatography-mass spectrometry through comparison to a synthetic standard. Further confirmation was obtained by forming a dimethoxyoxazole derivative by condensation of DMC with methylene chloride and through examination of methylated derivatives. DMC and DMH may serve as ferric chelators, oxygen-reducing agents, and redox-cycling molecules, which would include functioning as electron transport carriers to Fenton's reactions. Thus, they appear to be important components of the brown rot decay system of the fungus.

1,4-benzoquinone reductase from Phanerochaete chrysosporium: cDNA cloning and regulation of expression

A cDNA clone encoding a quinone reductase (QR) from the white rot basidiomycete Phanerochaete chrysosporium was isolated and sequenced. The cDNA consisted of 1,007 nucleotides and a poly(A) tail and encoded a deduced protein containing 271 amino acids. The experimentally determined eight-amino-acid N-terminal sequence of the purified QR protein from P. chrysosporium matched amino acids 72 to 79 of the predicted translation product of the cDNA. The Mr of the predicted translation product, beginning with Pro-72, was essentially identical to the experimentally determined Mr of one monomer of the QR dimer, and this finding suggested that QR is synthesized as a proenzyme. The results of in vitro transcription-translation experiments suggested that QR is synthesized as a proenzyme with a 71-amino-acid leader sequence. This leader sequence contains two potential KEX2 cleavage sites and numerous potential cleavage sites for dipeptidyl aminopeptidase. The QR activity in cultures of P. chrysosporium increased following the addition of 2-dimethoxybenzoquinone, vanillic acid, or several other aromatic compounds. An immunoblot analysis indicated that induction resulted in an increase in the amount of QR protein, and a Northern blot analysis indicated that this regulation occurs at the level of the qr mRNA.

Degradation of 2,4,6-trichlorophenol by Phanerochaete chrysosporium: involvement of reductive dechlorination

Under secondary metabolic conditions, the lignin-degrading basidiomycete Phanerochaete chrysosporium mineralizes 2,4, 6-trichlorophenol. The pathway for the degradation of 2,4, 6-trichlorophenol has been elucidated by the characterization of fungal metabolites and oxidation products generated by purified lignin peroxidase (LiP) and manganese peroxidase (MnP). The multistep pathway is initiated by a LiP- or MnP-catalyzed oxidative dechlorination reaction to produce 2,6-dichloro-1,4-benzoquinone. The quinone is reduced to 2,6-dichloro-1,4-dihydroxybenzene, which is reductively dechlorinated to yield 2-chloro-1,4-dihydroxybenzene. The latter is degraded further by one of two parallel pathways: it either undergoes further reductive dechlorination to yield 1, 4-hydroquinone, which is ortho-hydroxylated to produce 1,2, 4-trihydroxybenzene, or is hydroxylated to yield 5-chloro-1,2, 4-trihydroxybenzene, which is reductively dechlorinated to produce the common key metabolite 1,2,4-trihydroxybenzene. Presumably, the latter is ring cleaved with subsequent degradation to CO2. In this pathway, the chlorine at C-4 is oxidatively dechlorinated, whereas the other chlorines are removed by a reductive process in which chlorine is replaced by hydrogen. Apparently, all three chlorine atoms are removed prior to ring cleavage. To our knowledge, this is the first reported example of aromatic reductive dechlorination by a eukaryote.

Degradation of chlorophenoxyacetic acids by the lignin-degrading fungus Dichomitus squalens

Summary: We have examined the degradation of 14C ring- and side-chain-labelled 2,4,5-trichlorophenoxyacetic acid by Dichomitus squalens and Phanerochaete chrysosporium. The effects of Mn2+ on the degradation of these radiolabeled substrates by D. squalens and the effect of nitrogen limitation on their degradation by D. chrysosporium suggested that in both fungi, side-chain cleavage was catalysed by a mechanism independent of the lignin degradation system, whereas the degradation of the aromatic ring was dependent on the lignin degradative system. Using unlabelled substrates, a pathway for the degradation of chlorophenoxyacetic acids was elucidated in D. squalens. Time courses for the degradation of unlabelled chlorophenoxyacetic acids by D. squalens demonstrated that the corresponding chlorophenol was the initial product formed. The chlorophenol intermediate was xylosylated to form the chlorophenolxyloside. In turn, the chlorophenolxyloside could be hydrolysed by an intracellular -xylosidase to regenerate the chlorophenol. The chlorophenol product of the xylosidase reaction was oxidatively dechlorinated to form 2-chloro-p-benzoquinone which could undergo subsequent further dechlorination and ring-opening reactions, as has been reported previously for P. chrysosporium.

Dissecting the Diphenylene Iodonium-Sensitive NAD(P)H:Quinone Oxidoreductase of Zucchini Plasma Membrane

Quinone oxidoreductase activities dependent on pyridine nucleotides are associated with the plasma membrane (PM) in zucchini (Cucurbita pepo L.) hypocotyls. In the presence of NADPH, lipophilic ubiquinone homologs with up to three isoprenoid units were reduced by intact PM vesicles with a Km of 2 to 7 [mu]M. Affinities for both NADPH and NADH were similar (Km of 62 and 51 [mu]M, respectively). Two NAD(P)H:quinone oxidoreductase forms were identified. The first, labeled as peak I in gel-filtration experiments, behaves as an intrinsic membrane complex of about 300 kD, it slightly prefers NADH over NADPH, it is markedly sensitive to the inhibitor diphenylene iodonium, and it is active with lipophilic quinones. The second form (peak II) is an NADPH-preferring oxidoreductase of about 90 kD, weakly bound to the PM. Peak II is diphenylene iodonium-insensitive and resembles, in many properties, the soluble NAD(P)H:quinone oxidoreductase that is also present in the same tissue. Following purification of peak I, however, the latter gave rise to a quinone oxidoreductase of the soluble type (peak II), based on substrate and inhibitor specificities and chromatographic and electrophoretic evidence. It is proposed that a redox protein of the same class as the soluble NAD(P)H:quinone oxidoreductase (F. Sparla, G. Tedeschi, and P. Trost [1996] Plant Physiol. 112:249-258) is a component of the diphenylene iodonium-sensitive PM complex capable of reducing lipophilic quinones.

Quinone redox cycling in the ligninolytic fungus Pleurotus eryngii leading to extracellular production of superoxide anion radical

Quinone redox cycling is generally known as an intracellular process that implies the reduction of quinones (Q) into semiquinones (Q-.) or hydroquinones (QH2), which autoxidize reducing oxygen to superoxide anion radical (O-.2). We demonstrate here for the first time the existence of quinone redox cycling in a ligninolytic fungus, Pleurotus eryngii, showing two particularities: extracellular production of O-.2 and involvement of ligninolytic enzymes. Experiments were performed with P. eryngii cultures, showing laccase activity, and four quinones: 1,4-benzoquinone (BQ), 2-methyl-1,4-benzoquinone (MeBQ), 2,3,5,6-tetramethyl-1,4-benzoquinone (duroquinone, DQ), and 2-methyl-1,4-naphthoquinone (menadione, MD). The overall process consisted of cell-bound divalent reduction of quinones, followed by extracellular laccase-mediated oxidation of hydroquinones into semiquinones, which autoxidized to a certain extent producing O-.2 (at the pH values of natural degradation of lignin, some autoxidation of hydroquinones was observed only with DQH2 and MDH2). The existence of a redox cyclic system involving quinones was evidenced by determining the chemical state of quinones along incubation under several conditions (either different O2 concentrations and pH values or laccase amounts). Thus, QH2/Q ratios at system equilibrium decreased as either pH values and oxygen concentration (allowing hydroquinones autoxidation) or the amount of laccase increased. Once the cyclic nature of the system was demonstrated, special attention was paid to the production of O-.2 during hydroquinone oxidation. Except in the case of BQH2, production of O-.2 was found in samples containing hydroquinones and laccase. By the use of agents promoting the autoxidation of semiquinones (superoxide dismutase and Mn2+), production of O-.2 during oxidation of BQH2 could finally be demonstrated.

NAD(P)H:(Quinone-Acceptor) Oxidoreductase of Tobacco Leaves Is a Flavin Mononucleotide-Containing Flavoenzyme

The soluble NAD(P)H:(quinone-acceptor) oxidoreductase [NAD(P)H-QR, EC 1.6.99.2] of Nicotiana tabacum L. leaves and roots has been purified. NAD(P)H-QR contains noncovalently bound flavin mononucleotide. Pairs of subunits of 21.4 kD are linked together by disulfide bridges, but the active enzyme is a homotetramer of 94 to 100 kD showing an isoelectric point of 5.1. NAD(P)H-QR is a B-stereospecific dehydrogenase. NADH and NADPH are electron donors of similar efficiency with Kcat:Km ratios (with duroquinone) of 6.2 x 107 and 8.0 x 107 m-1 s-1, respectively. Hydrophilic quinones are good electron acceptors, although ferricyanide and dichlorophenolindophenol are also reduced. The quinones are converted to hydroquinones by an obligatory two-electron transfer. No spectral evidence for a flavin semiquinone was detected following anaerobic photoreduction. Cibacron blue and 7-iodo-acridone-4-carboxylic acid are inhibitory. Tobacco NAD(P)H-QR resembles animal DT-diaphorase in some respects (identical reaction mechanism with a two-electron transfer to quinones, unusually high catalytic capability, and donor and acceptor substrate specificity), but it differs from DT-diaphorase in molecular structure, flavin cofactor, stereospecificity, and sensitivity to inhibitors. As in the case with DT-diaphorase in animals, the main NAD(P)H-QR function in plant cells may be the reduction of quinones to quinols, which prevents the production of semiquinones and oxygen radicals. The enzyme appears to belong to a widespread group of plant and fungal flavoproteins found in different cell compartments that are able to reduce quinones.