Complete decolorization of the anthraquinone dye Reactive blue 5 by the concerted action of two peroxidases from Thanatephorus cucumeris Dec 1

Characterization of three novel DyP-type peroxidases from Streptomyces chartreusis NRRL 3882

AIMS

Actinobacteria are known to produce extracellular enzymes including DyPs. We set out to identify and characterize novel peroxidases from Streptomyces chartreusis NRRL 3882, because S. chartreusis belongs to the small group of actinobacteria with three different DyPs.

METHODS AND RESULTS

The genome of the actinomycete Streptomyces chartreusis NRRL 3882 was mined for novel DyP-type peroxidases. Three genes encoding for DyP-type peroxidases were cloned and overexpressed in Escherichia coli. Subsequent characterization of the recombinant proteins included examination of operating conditions such as pH, temperature, and H₂ O₂ concentrations, as well as substrate spectrum. Despite their high sequence similarity, the enzymes named SCDYP1-SCDYP3 presented distinct preferences regarding their operating conditions. They showed great divergence in H₂ O₂ tolerance and stability, with SCDYP2 being most active at concentrations above 50 mmol l^-1 . Moreover, SCDYP1 and SCDYP3 preferred acidic pH (typical for DyP-type peroxidases) whereas SCDYP2 was most active at pH 8.

CONCLUSIONS

Regarding the function of DyPs in nature, these results suggest that availability of different DyP variants with complementary activity profiles in one organism might convey evolutionary benefits.

SIGNIFICANCE AND IMPACT OF STUDY

DyP-type peroxidases are able to degrade xenobiotic compounds and thus can be applied in biocatalysis and bioremediation. However, the native function of DyPs and the benefits for their producers largely remain to be elucidated.

Widespread Ability of Ligninolytic Fungi to Degrade Hazardous Organic Pollutants as the Basis for the Self-Purification Ability of Natural Ecosystems and for Mycoremediation Technologies

The ability of sixteen wood- and soil-inhabiting basidiomycete strains and four ascomycete strains to degrade the most hazardous, widespread, and persistent pollutants (polycyclic aromatic hydrocarbons, oxyethylated nonylphenol, alkylphenol, anthraquinone-type synthetic dyes, and oil) was found. The disappearance of the pollutants, their main metabolites, and some adaptive properties (activities of ligninolytic enzymes, the production of emulsifying compounds and exopolysaccharides) were evaluated. The toxicity of polycyclic aromatic hydrocarbons decreased during degradation. New data were obtained regarding (1) the dependence of the completeness of polycyclic aromatic hydrocarbon degradation on the composition of the ligninolytic enzyme complex; (2) the degradation of neonol AF9-12 by higher fungi (different accessibilities of the oxyethyl chain and the aromatic ring of the molecules to different fungal genera); and (3) the production of an emulsifying agent in response to the presence in the cultivation medium of hydrophobic pollutants as the common property of wood- and soil-inhabiting basidiomycetes and ascomycetes. Promise for use in mycoremediation was shown in the wood-inhabiting basidiomycetes Pleurotus ostreatus f. Florida, Schizophyllum commune, Trametes versicolor MUT 3403, and Trametes versicolor DSM11372; the litter-decomposing basidiomycete Stropharia rugosoannulata; and the ascomycete Cladosporium herbarum. These fungi degrade a wide range of pollutants without accumulation of toxic metabolites and produce ligninolytic enzymes and emulsifying compounds.

Transformation of Reactive Blue 19 by a recombinant peroxidase DyP

Wastewater containing recalcitrant dyes causes environmental problems. A new superfamily of heme-containing peroxidases, dye-decolorizing peroxidases (DyPs), has been found to decolorize different kinds of dyes, especial anthraquinone dyes efficiently. However, the mechanism of dyes degradation by DyPs has not been fully understood and the toxicity of dye degradation intermediates by DyPs catalysis to microbes is unclear. In this study, a purified recombinant Thermobifida fusca DyP (TfuDyP) in E. coli BL21(DE3) was used to treat Reactive Blue 19 (RB19), an anthraquinone dye. The reaction intermediates analyzed by ultra performance liquid chromatography/mass spectroscopy (UPLC-MS) indicated the initial site of TfuDyP attack on RB19. In addition, it was found that both RB19 and its incomplete degradation products inhibited the growth of Bacillus subtilis. These findings provided a novel understanding of DyPs catalysis to anthraquinone dyes.

DyP-Type Peroxidases: Recent Advances and Perspectives

In this review, we chart the major milestones in the research progress on the DyP-type peroxidase family over the past decade. Though mainly distributed among bacteria and fungi, this family actually exhibits more widespread diversity. Advanced tertiary structural analyses have revealed common and different features among members of this family. Notably, the catalytic cycle for the peroxidase activity of DyP-type peroxidases appears to be different from that of other ubiquitous heme peroxidases. DyP-type peroxidases have also been reported to possess activities in addition to peroxidase function, including hydrolase or oxidase activity. They also show various cellular distributions, functioning not only inside cells but also outside of cells. Some are also cargo proteins of encapsulin. Unique, noteworthy functions include a key role in life-cycle switching in Streptomyces and the operation of an iron transport system in Staphylococcus aureus, Bacillus subtilis and Escherichia coli. We also present several probable physiological roles of DyP-type peroxidases that reflect the widespread distribution and function of these enzymes. Lignin degradation is the most common function attributed to DyP-type peroxidases, but their activity is not high compared with that of standard lignin-degrading enzymes. From an environmental standpoint, degradation of natural antifungal anthraquinone compounds is a specific focus of DyP-type peroxidase research. Considered in its totality, the DyP-type peroxidase family offers a rich source of diverse and attractive materials for research scientists.

Investigation of reactive Blue 19 biodegradation and byproducts toxicity assessment using crude laccase extract from Trametes versicolor

Crude laccase potency on biodegradation and detoxification of Reactive blue 19 (RB-19) were demonstrated, along with prediction of degradation mechanisms, pathways and byproducts analysis. Trametes versicolor, cultured on pampas grass inflorescence (Cortaderia selloana), yielded the best crude laccase activity (15.36 U/g). 10 U CLE activities demonstrated a biodegradation yield (85%) in 210 min, at pH 4, 50 °C and 200 mg/L RB-19 concentrations. Evolution of a brown color that absorbed maximally at 478 nm was observed during biodegradation. Two methods were adopted for byproducts extraction, three methods for toxicity analysis and four models for kinetic parameters (K_m and V_max) determination. 2-ethylanthracene, 2-hydroxycyclohexa-2,4-dien-1-one, 2(4-methylphenyl)-ethan-1-amine, 1-[6-hydroperoxy-4,5-bis(sulfooxy)oxan-3-yl]triaza-1,2-dien-2-ium, naphthalene-2,7-disulfonic acid and N-[(5-oxooxolan-2-yl)methyl]acetamide were detected as toxic byproducts. Brown color evolution was due to 1,1,1-triethyl-3-(methoxycarbonyl)-2,2-dioxo-2λ6-diazathian-1-ium (methoxycarbonyl sulfanyl-triethylammonium hydroxide) inner salt. Increase in color density (light to dark brown) was a function of byproduct(s) biodegradation and polymerization. RB-19 and byproduct acute toxicities were decreased significantly (98% - 6.91%). Kinetic parameters K_m (18.05 mg/L) and V_max (0.31 mg/L. min^-1) from the four kinetic models demonstrated higher affinity of CLE to RB-19. CLE yielded a catalytic activity (V_max/K_m =0.017 min^-1) demonstrating the flexibility of CLE active site to RB-19 binding over commercial laccase.

Growth conditions, physiological properties, and selection of optimal parameters of biodegradation of anticancer drug daunomycin in industrial effluents by Bjerkandera adusta CCBAS930

The study characterizes the anamorphic Bjerkandera adusta strain CCBAS 930, including growth conditions, physiological properties, and enzymatic activities related to basic metabolism and specific properties coupled with the fungal secondary metabolism. It was established that the fungus grows in a wide pH range (3.5-7.5), up to 3% of salt concentration and a temperature of 5-30 °C. Media rich in natural organic components (potato, maize extracts, whey) are optimal for biomass propagation. Minimal media, containing mineral salts and glucose as well as static growth conditions, are required to obtain idiophasic mycelium, equivalent to the secondary metabolism of the fungus. Of the 7 complex C, N, and energy sources tested, the strain did not utilize only fibrous cellulose. Lipolytic activity reached the highest values of the enzymatic activities corresponding to those capabilities. The specific properties of strain B. adusta CCBAS 930 determined by the production of HRP-like peroxidase were related to the decolorization and biodegradation of anthraquinone derivative daunomycin. The decolorization of 30% of daunomycin effluents occurred most rapidly in iso-osmotic medium and non-enriched with nitrogen, containing 0.25% glucose, pH = 5.0-6.0, and 25-30 °C. In agitated cultures, the strain decolorized solutions of daunomycin by biosorption, which coincided with the inhibition of aerial mycelium production and HRP-like biosynthesis. Based on knowledge, potential and real possibilities of using the strain in bioremediation of colored industrial sewage were discussed.

Degradation of antifungal anthraquinone compounds is a probable physiological role of DyP secreted by Bjerkandera adusta

Alizarin is an anti-fungal compound produced by the plant, Rubia tinctorum. The parasitic fungus Bjerkandera adusta Dec 1 was cultured in potato dextrose (PD) medium with or without alizarin. Alizarin was a good substrate for the dye-decolorizing peroxidase (DyP) from B. adusta Dec 1 and hampered B. adusta growth at the early stage of plate culture. During liquid shaking culture, DyP activity in cultures supplemented with 100 μM alizarin was greater than that in controls cultured without alizarin. In particular, DyP activity per dry cell mass increased approximately 3.5-, 3.1-, and 2.9-fold at 24, 30, and 36 h after inoculation, respectively, compared with control cultures. These data suggest that alizarin stimulates the expression of DyP. Interestingly, alizarin rapidly decomposed at an early stage in culture (24–42 h) in PD medium supplemented with 100 μM alizarin. Thus, alizarin appears to induce DyP expression in B. adusta Dec 1, and this DyP, in turn, rapidly degrades alizarin. Collectively, our findings suggest that the physiological role of DyP is to degrade antifungal compounds produced by plants.

The degradative activity and adaptation potential of the litter-decomposing fungus Stropharia rugosoannulata

The ability of the litter-decomposing basidiomycete Stropharia rugosoannulata DSM 11372 to degrade a wide range of structurally different environmental pollutants such as polycyclic aromatic hydrocarbons (PAHs: phenanthrene, anthracene, fluorene, pyrene, and fluoranthene), synthetic anthraquinone dyes containing condensed aromatic rings, environmentally relevant alkylphenol and oxyethylated alkylphenol representatives, and oil was demonstrated within the present study. 9,10-Anthraquinone, phenanthrene-9,10-quinone, and 9-fluorenone were identified as products of anthracene, phenanthrene, and fluorene degradation, respectively. Fungal degradation was accompanied by the production of the ligninolytic enzymes: laccase and Mn peroxidase, suggesting their involvement in pollutant degradation. Extracellular polysaccharide(s) (EPS) and emulsifying compound(s) were concomitantly produced. EPS composed of mannose, glucose, and galactose was isolated from the cultivation medium, and its effects on catalytic properties of purified laccase from S. rugosoannulata (the dominating ligninolytic enzyme under the applied conditions) were studied. A simultaneous decrease of K_M and V_max values observed for the enzymatic oxidation of non-phenolic (2,2-azino-bis-(3-ethylbenzthiazoline-6-sulphonic acid) diammonium salt; ABTS) and phenolic compounds (2,6-dimethoxyphenol) in presence of EPS suggest an interaction of EPS and laccase resulting in a modulation of the catalytic performance of the enzyme, which has, to the best of our knowledge, not been reported before. In line with such a modulation, the laccase-catalyzed oxidation of natural aromatic compounds (veratryl alcohol, adlerol) and environmental pollutants (the alkylphenol representative nonylphenol, the diphenylmethane derivative bisphenol A, and the PAH representative anthracene) was found to be enhanced in presence of EPS. The relevance of such effects for real environmental processes and their implications remain to be investigated.

Identification, heterologous expression and characterization of a dye-decolorizing peroxidase of Pleurotus sapidus

The coding sequence of a peroxidase from the secretome of Pleurotus sapidus was cloned from a cDNA library. Bioinformatic analyses revealed an open reading frame of 1551 bp corresponding to a primary translation product of 516 amino acids. The DyP-type peroxidase was heterologously produced in Trichoderma reesei with an activity of 55,000 U L^-1. The enzyme was purified from the culture supernatant, biochemically characterized and the kinetic parameters were determined. The enzyme has an N-terminal signal peptide composed of 62 amino acids. Analysis by Blue Native PAGE and activity staining with ABTS, as well as gel filtration chromatography showed the native dimeric state of the enzyme (115 kDa). Analysis of the substrate range revealed that the recombinant enzyme catalyzes, in addition to the conversion of some classic peroxidase substrates such as 2,2'-azino-bis(3-ethylthiazoline-6-sulfonate) and substituted phenols like 2,6-dimethoxyphenol, also the decolorization of the anthraquinonic dye Reactive Blue 5. The enzyme also catalyzes bleaching of natural colorants such as β-carotene and annatto. Surprisingly, β-carotene was transformed in the presence and absence of H₂O₂ by rPsaDyP, however enzyme activity was increased by the addition of H₂O₂. This indicates that the rPsaDyP has an oxidase function in addition to a peroxidase activity. As a consequence of the high affinity to the characteristic substrate Reactive Blue 5 the rPsaDyP belongs functionally to the dyp-type peroxidase family.

Stable ABTS Immobilized in the MIL-100(Fe) Metal-Organic Framework as an Efficient Mediator for Laccase-Catalyzed Decolorization

The successful encapsulation of 2,2′-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS), a well-known laccase mediator, within a mesoporous metal-organic framework sample (i.e., MIL-100(Fe)) was achieved using a one-pot hydrothermal synthetic method. The as-prepared ABTS@MIL-100(Fe) was characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD), Fourier transform infrared (FT-IR) spectroscopy, nitrogen sorption, and cyclic voltammetry (CV). Our ABTS@MIL-100(Fe)-based electrode exhibited an excellent electrochemical response, indicating that MIL-100(Fe) provides an appropriate microenvironment for the immobilization and electroactivity of ABTS molecules. ABTS@MIL-100(Fe) was then evaluated as an immobilized laccase mediator for dye removal using indigo carmine (IC) as a model dye. Through the application of laccase in combination with a free (ABTS) or immobilized (ABTS@MIL-100(Fe)) mediator, decolorization yields of 95% and 94%, respectively, were obtained for IC after 50 min. In addition, following seven reuse cycles of ABTS@MIL-100(Fe) for dye treatment, a decolorization yield of 74% was obtained. Dye decolorization occurred through the breakdown of the chromophoric group by the Laccase/ABTS@MIL-100(Fe) system, and a catalytic mechanism was proposed. We therefore expect that the stability, reusability, and validity of ABTS@MIL-100(Fe) as a laccase mediator potentially render it a promising tool for dye removal, in addition to reducing the high running costs and potential toxicity associated with synthetic mediators.

Identification of a Novel Dye-Decolorizing Peroxidase, EfeB, Translocated by a Twin-Arginine Translocation System in Streptococcus thermophilus CGMCC 7.179

Streptococcus thermophilus is a facultative anaerobic bacterium that has the ability to grow and survive in aerobic environments, but the mechanism for this remains unclear. In this study, the efeB gene, encoding a dye-decolorizing peroxidase, was identified in the genome of Streptococcus thermophilus CGMCC 7.179, and purified EfeB was able to decolorize reactive blue 5. Strikingly, genes encoding two components (TatA and TatC) of the twin-arginine translocation (TAT) system were also found in the same operon with the efeB gene. Knocking out efeB or tatC resulted in decreased growth of the strain under aerobic conditions, and complementation of the efeB-deficient strains with the efeB gene enhanced the biomass of the hosts only in the presence of the tatC gene. Moreover, it was proved for both S. thermophilus CGMCC 7.179 and Escherichia coli DE3 that EfeB could be translocated by the TAT system of S. thermophilus. In addition, the transcriptional levels of efeB and tatC increased when the strain was cultured under aerobic conditions. Overall, these results provide the first evidence that EfeB plays a role in protecting cells of S. thermophilus from oxidative stress, with the assistance of the TAT system.

Redox-Active Sites in Auricularia auricula-judae Dye-Decolorizing Peroxidase and Several Directed Variants: A Multifrequency EPR Study

Peroxide-activated Auricularia auricula-judae dye-decolorizing peroxidase (DyP) forms a mixed Trp377 and Tyr337 radical, the former being responsible for oxidation of the typical DyP substrates (Linde et al. Biochem. J., 2015, 466, 253-262); however, a pure tryptophanyl radical EPR signal is detected at pH 7 (where the enzyme is inactive), in contrast with the mixed signal observed at pH for optimum activity, pH 3. On the contrary, the presence of a second tyrosine radical (at Tyr147) is deduced by a multifrequency EPR study of a variety of simple and double-directed variants (including substitution of the above and other tryptophan and tyrosine residues) at different freezing times after their activation by H2O2 (at pH 3). This points out that subsidiary long-range electron-transfer pathways enter into operation when the main pathway(s) is removed by directed mutagenesis, with catalytic efficiencies progressively decreasing. Finally, self-reduction of the Trp377 neutral radical is observed when reaction time (before freezing) is increased in the absence of reducing substrates (from 10 to 60 s). Interestingly, the tryptophanyl radical is stable in the Y147S/Y337S variant, indicating that these two tyrosine residues are involved in the self-reduction reaction.

Substrate, product, and cofactor: The extraordinarily flexible relationship between the CDE superfamily and heme

PFam Clan 0032, also known as the CDE superfamily, is a diverse group of at least 20 protein families sharing a common α,β-barrel domain. Of these, six different groups bind heme inside the barrel's interior, using it alternately as a cofactor, substrate, or product. Focusing on these six, an integrated picture of structure, sequence, taxonomy, and mechanism is presented here, detailing how a single structural motif might be able to mediate such an array of functions with one of nature's most important small molecules.

Description of the first fungal dye-decolorizing peroxidase oxidizing manganese(II)

Two phylogenetically divergent genes of the new family of dye-decolorizing peroxidases (DyPs) were found during comparison of the four DyP genes identified in the Pleurotus ostreatus genome with over 200 DyP genes from other basidiomycete genomes. The heterologously expressed enzymes (Pleos-DyP1 and Pleos-DyP4, following the genome nomenclature) efficiently oxidize anthraquinoid dyes (such as Reactive Blue 19), which are characteristic DyP substrates, as well as low redox-potential dyes (such as 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid)) and substituted phenols. However, only Pleos-DyP4 oxidizes the high redox-potential dye Reactive Black 5, at the same time that it displays high thermal and pH stability. Unexpectedly, both enzymes also oxidize Mn²⁺ to Mn³⁺, albeit with very different catalytic efficiencies. Pleos-DyP4 presents a Mn²⁺ turnover (56 s⁻¹) nearly in the same order of the two other Mn²⁺-oxidizing peroxidase families identified in the P. ostreatus genome: manganese peroxidases (100 s⁻¹ average turnover) and versatile peroxidases (145 s⁻¹ average turnover), whose genes were also heterologously expressed. Oxidation of Mn²⁺ has been reported for an Amycolatopsis DyP (24 s⁻¹) and claimed for other bacterial DyPs, albeit with lower activities, but this is the first time that Mn²⁺ oxidation is reported for a fungal DyP. Interestingly, Pleos-DyP4 (together with ligninolytic peroxidases) is detected in the secretome of P. ostreatus grown on different lignocellulosic substrates. It is suggested that generation of Mn³⁺ oxidizers plays a role in the P. ostreatus white-rot lifestyle since three different families of Mn²⁺-oxidizing peroxidase genes are present in its genome being expressed during lignocellulose degradation.

Basidiomycete DyPs: Genomic diversity, structural-functional aspects, reaction mechanism and environmental significance

The first enzyme with dye-decolorizing peroxidase (DyP) activity was described in 1999 from an arthroconidial culture of the fungus Bjerkandera adusta. However, the first DyP sequence had been deposited three years before, as a peroxidase gene from a culture of an unidentified fungus of the family Polyporaceae (probably Irpex lacteus). Since the first description, fewer than ten basidiomycete DyPs have been purified and characterized, but a large number of sequences are available from genomes. DyPs share a general fold and heme location with chlorite dismutases and other DyP-type related proteins (such as Escherichia coli EfeB), forming the CDE superfamily. Taking into account the lack of an evolutionary relationship with the catalase-peroxidase superfamily, the observed heme pocket similarities must be considered as a convergent type of evolution to provide similar reactivity to the enzyme cofactor. Studies on the Auricularia auricula-judae DyP showed that high-turnover oxidation of anthraquinone type and other DyP substrates occurs via long-range electron transfer from an exposed tryptophan (Trp377, conserved in most basidiomycete DyPs), whose catalytic radical was identified in the H2O2-activated enzyme. The existence of accessory oxidation sites in DyP is suggested by the residual activity observed after site-directed mutagenesis of the above tryptophan. DyP degradation of substituted anthraquinone dyes (such as Reactive Blue 5) most probably proceeds via typical one-electron peroxidase oxidations and product breakdown without a DyP-catalyzed hydrolase reaction. Although various DyPs are able to break down phenolic lignin model dimers, and basidiomycete DyPs also present marginal activity on nonphenolic dimers, a significant contribution to lignin degradation is unlikely because of the low activity on high redox-potential substrates.

Trametes meyenii possesses elevated dye degradation abilities under normal nutritional conditions compared to other white rot fungi

Several species of white-rot fungi were investigated for their utility in prolonged decolouration of the recalcitrant sulfonated azo dye, amaranth. Trametes pubescens, T. multicolor, T. meyenii and T. versicolor decoloured amaranth azo-dye best on low-nitrogen agar-solidified media whereas Bjerkandera adusta and Phlebia radiata were most effective in low nitrogen medium supplemented with manganese. Trametes cotonea did not decolour effectively under any condition. The decolouring Trametes species were also effective in liquid culture whereas B. adusta and P. radiata were not. Trametes meyenii, T. pubescens and T. multicolor were equal to or better than commonly employed T. versicolor at decolouring amaranth. This is the first study to show the dye decolouration potential of T. meyenii, T. pubescens, and T. multicolor. Supplementing with Mn(II) increased assayable manganese peroxidase activity, but not long-term decolouration, indicating that laccase is the main decolourizing enzyme in these Trametes species. This appears to be because of inadequate Mn(3+) chelation required by manganese peroxidase because adding relatively low amounts of malonate enhanced decolouration rates. The ability of Trametes meyenii to simultaneously decolour dye over prolonged periods of time while growing in relatively nutrient-rich medium appears to be unique amongst white-rot fungi, indicating its potential in wastewater bioremediation.

Anthraquinone dyes decolorization capacity of anamorphic Bjerkandera adusta CCBAS 930 strain and its HRP-like negative mutants

Cultures of the anamorphic fungus Bjerkandera adusta CCBAS 930 decolorizing, in stationary cultures, 0.01 % solutions of carminic acid and Poly R-478, were characterised by a strong increase in the activity of the horseradish peroxidase (HRP-like) and manganese-dependent peroxidase (MnP) at a low activity of lignin peroxidase. Genotypically modified mutants of B. adusta CCBAS 930: 930-5 and 930-14, with total or partial loss of decolorization capabilities relative to anthraquinonic dyes, showed inhibition of the activity of HRP-like peroxidase and MnP. Whereas, compared to the parental strain, in the mutant cultures there was an increase in the activity of lignin peroxidase and laccase. The paper presents a discussion of the role of the studied enzymatic activities in the process of decolorization of anthraquinonic dyes by the strain B. adusta CCBAS 930.

Expression, purification and crystallization of a dye-decolourizing peroxidase from Dictyostelium discoideum

Dye-decolourizing peroxidases are haem-containing peroxidases with broad substrate specificity. Using H2O2 as an electron acceptor, they efficiently decolourize various dyes that are of industrial and environmental relevance, such as anthraquninone- and azo-based dyes. In this study, the dye-decolourizing peroxidase DdDyP from Dictyostelium discoideum was overexpressed in Escherichia coli strain Rosetta(DE3)pLysS, purified and crystallized using the vapour-diffusion method. A native crystal diffracted to 1.65 Å resolution and belonged to space group P4(1)2(1)2, with unit-cell parameters a = b = 141.03, c = 95.56 Å, α = β = γ = 90°. The asymmetric unit contains two molecules.

Peroxidase(s) in environment protection

Industrial discharges of untreated effluents into water bodies and emissions into air have deteriorated the quality of water and air, respectively. The huge amount of pollutants derived from industrial activities represents a threat for the environment and ecologic equilibrium. Phenols and halogenated phenols, polycyclic aromatic hydrocarbons (PAH), endocrine disruptive chemicals (EDC), pesticides, dioxins, polychlorinated biphenyls (PCB), industrial dyes, and other xenobiotics are among the most important pollutants. Peroxidases are enzymes that are able to transform a variety of compounds following a free radical mechanism, thereby yielding oxidized or polymerized products. The peroxidase transformation of these pollutants is accompanied by a reduction in their toxicity, due to loss of biological activity, reduction in the bioavailability, or the removal from aqueous phase, especially when the pollutant is found in water. The review describes the sources of peroxidases, the reactions catalyzed by them, and their applications in the management of pollutants in the environment.

Identification and characterization of a multifunctional dye peroxidase from a lignin-reactive bacterium

Plant biomass represents a renewable feedstock that has not yet been fully tapped because of the difficulty in accessing the carbon in its structural biopolymers. Lignin is an especially challenging substrate, but select microbes have evolved complex systems of enzymes for its breakdown through a radical-mediated oxidation process. Fungal systems are well-characterized for their ability to depolymerize lignin, but the ability of bacteria to react with this substrate remains elusive. We have therefore focused on elucidating strategies used by lignin-reactive soil bacteria and describing their oxidative enzyme systems. We now report the identification and characterization of an unusual C-type dye-decolorizing peroxidase from Amycolatopsis sp. 75iv2 (DyP2), which belongs to a family of heme peroxidases reported to be involved in bacterial lignin degradation. Biochemical studies indicate that DyP2 has novel function for this family, with versatile and high activity both as a peroxidase and Mn peroxidase (k(cat)/K(M) ≈ 10(5)-10(6) M(-1) s(-1)). It also has a Mn-dependent oxidase mode of action that expands its substrate scope. Crystallographic studies of DyP2 at 2.25 Å resolution show the existence of a Mn binding pocket and support its key role in catalysis.

First crystal structure of a fungal high-redox potential dye-decolorizing peroxidase: substrate interaction sites and long-range electron transfer

Dye-decolorizing peroxidases (DyPs) belong to the large group of heme peroxidases. They utilize hydrogen peroxide to catalyze oxidations of various organic compounds. AauDyPI from Auricularia auricula-judae (fungi) was crystallized, and its crystal structure was determined at 2.1 Å resolution. The mostly helical structure also shows a β-sheet motif typical for DyPs and Cld (chlorite dismutase)-related structures and includes the complete polypeptide chain. At the distal side of the heme molecule, a flexible aspartate residue (Asp-168) plays a key role in catalysis. It guides incoming hydrogen peroxide toward the heme iron and mediates proton rearrangement in the process of Compound I formation. Afterward, its side chain changes its conformation, now pointing toward the protein backbone. We propose an extended functionality of Asp-168, which acts like a gatekeeper by altering the width of the heme cavity access channel. Chemical modifications of potentially redox-active amino acids show that a tyrosine is involved in substrate interaction. Using spin-trapping experiments, a transient radical on the surface-exposed Tyr-337 was identified as the oxidation site for bulky substrates. A possible long-range electron transfer pathway from the surface of the enzyme to the redox cofactor (heme) is discussed.

Identification and molecular characterization of a novel DyP-type peroxidase from Pseudomonas aeruginosa PKE117

A new DyP-type peroxidase from Pseudomonas aeruginosa PKE117 was identified and characterized. The dypPa was first identified via sequence analysis and then cloned in Escherichia coli. Subsequently, the recombinant protein DyPPa was expressed and purified. Its DNA sequence analysis revealed an open reading frame of 897 bp, encoding a protein monomer of 299 amino acid residues with isoelectric point 4.62. According to SDS-PAGE analysis and FPLC result, DyPPa mainly existed as homodimer (64 kDa). DyPPa displayed typical heme absorbance of Soret band, with an Rz value of 1.18. Inductively coupled plasma-atomic absorption spectrum data also indicated DyPPa contained iron. Multiple amino acid sequence alignment of DyPPa with other members of the DyP-type peroxidases family showed the presence of conserved D139, H210, and R227 amino acids and GXXDG motifs, which were commonly shared by the DyP-type peroxidase family. Although the primary structure homology between DyPPa and other family members was very low, their secondary and tertiary structure displayed high homology, which explained the high decolorizing activity of DyPPa. Specifically, DyPPa displayed a good thermal stability and maximal activity on Reactive blue 5 under pH 3.5. Therefore, it was proposed that DyPPa, with a wide range of substrate specificity, was a novel member of the DyP-type peroxidases family.

Degradation of the synthetic dye amaranth by the fungus Bjerkandera adusta Dec 1: inference of the degradation pathway from an analysis of decolorized products

We examined the degradation of amaranth, a representative azo dye, by Bjerkandera adusta Dec 1. The degradation products were analyzed by high performance liquid chromatography (HPLC), visible absorbance, and electrospray ionization time-of-flight mass spectroscopy (ESI-TOF-MS). At the primary culture stage (3 days), the probable reaction intermediates were 1-aminonaphthalene-2,3,6-triol, 4-(hydroxyamino) naphthalene-1-ol, and 2-hydroxy-3-[2-(4-sulfophenyl) hydrazinyl] benzenesulfonic acid. After 10 days, the reaction products detected were 4-nitrophenol, phenol, 2-hydroxy-3-nitrobenzenesulfonic acid, 4-nitrobenzene sulfonic acid, and 3,4'-disulfonyl azo benzene, suggesting that no aromatic amines were created. Manganese-dependent peroxidase activity increased sharply after 3 days culture. Based on these results, we herein propose, for the first time, a degradation pathway for amaranth. Our results suggest that Dec 1 degrades amaranth via the combined activities of peroxidase and hydrolase and reductase action.

Efficient industrial dye decolorization by Bacillus sp. VUS with its enzyme system

This work presents role of different enzymes in decolorization of industrial dye Orange T4LL by Bacillus sp. VUS. Bacillus sp. strain VUS decolorized dye Orange T4LL, under static anoxic condition in 24 h. During decolorization of Orange T4LL a significant induction in the activities of lignin peroxidase, tyrosinase, and reductases (NADH-DCIP, azo, and riboflavin) was observed. The biodegradation was monitored by Ultraviolet-visible spectroscopy, Fourier transform infrared spectroscopy, and high performance liquid chromatography. The final products 4-methyl-2-o-tolylazo-benzene-1,3-diamine and [3-(phenyl-hydrazono)-cyclohexa-1,4-dienyl]-methanol were characterized by gas chromatography-mass spectroscopy. Phytotoxicity, COD, and BOD revealed non-toxicity of degraded products. Phytotoxicity study demonstrated non-toxicity of the biodegraded products for crop plants with respect to Triticum aestivum and Sorghum bicolor. Bacillus sp. VUS with its enzyme system could be a useful tool for textile effluent treatment.

Decolorization and biodegradation of remazol brilliant blue R by bilirubin oxidase

The dye-decolorizing potential of bilirubin oxidase (BOX) was demonstrated for an anthraquinone dye, remazol brilliant blue R (RBBR). The dye was decolorized 40% within 4 h by the BOX alone, whereas it was more efficient in the presence of 2, 2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), showing 91.5% decolorization within 25 min. The effects of operational parameters on decolorization were examined. The results showed that the decolorization efficiency decreased with increasing RBBR concentration, and a marked inhibition effect was exhibited when the dye concentrations were above 100 mg l(-1). The optimum temperature for enzymatic decolorization was 40 degrees C. BOX showed efficient decolorization of the dye with a wide pH range of 5-8.5. The maximum decolorization activity occurred at pH 8 with ABTS and at pH 5 without ABTS. Analysis of RBBR ultraviolet and visible (UV-VIS) spectra after BOX treatment indicated that the decolorization of RBBR was due to biodegradation. Our results suggested that ABTS can serve as an electron mediator to facilitate the oxidation of RBBR, and the BOX-ABTS mediator-involved dye decolorization mechanism was similar to that of laccase. Operation over a wide range of pH and efficient decolorization suggested that the BOX can be used to decolorize synthetic dyes from effluents, especially for anthraquinonic dyes.

Application of statistical experimental methodology to optimize reactive dye decolourization by commercial laccase

Three-level Box-Behnken factorial design with three factors (pH, temperature and enzyme concentration) combined with response surface methodology (RSM) was applied to optimize the dye degradation of reactive red 239 (RR239), reactive yellow 15 (RY15) and reactive blue 114 (RB114) dyes by commercial laccase. Mathematical models were developed for each dye showing the effect of each factor and their interactions on colour removal. The model predicted for RY15 that a decolourization above 90% (after 24h) could be obtained when the enzyme concentration, temperature and pH were set at 109.8U/L, 39.2 degrees C and 6.6, respectively; whilst for RB114 and RR239 the temperature and enzyme concentration did not affect the decolourization (>90%) in the considered range and optimum pH value was found at 5.5-7.0 and 7.0-7.5, respectively. These predicted values were also experimentally validated. Average final values of responses were in good agreement with calculated values, thus confirming the reliability of the models of RY15, RB114 and RR239 decolourization.

Degradation pathway of an anthraquinone dye catalyzed by a unique peroxidase DyP from Thanatephorus cucumeris Dec 1

The reactants produced by action of a purified unique dye-decolorizing peroxidase, DyP, on a commercial anthraquinone dye, Reactive Blue 5, were investigated using electrospray ionization mass spectrometry (ESI-MS), thin-layer chromatography (TLC), and (1)H- and (13)C- nuclear magnetic resonance (NMR). The results of ESI-MS analysis showed that phthalic acid, a Product 2 (molecular weight 472.5), and a Product 3 (molecular weight 301.5), were produced. Product 2 and Product 3 were generated by usual peroxidase reaction, whereas phthalic acid was generated by hydrolase- or oxygenase-catalyzed reaction. One potential associated product, o-aminobenzene sulfonic acid, was found to be converted to 2,2'-disulfonyl azobenzene by ESI-MS and NMR analyses. From these results, we propose, for the first time, the degradation pathway of an anthraquinone dye by the enzyme DyP.

Coupling occurs before breakdown during biotransformation of Acid Blue 62 by white rot fungi

Only few data exist on the metabolites produced during the biotransformation of anthraquinonic dyes by white rot fungi (WRF). During the biotransformation of an anthraquinonic dye Acid Blue 62 (ABu62) using Pycnoporus sanguineus MUCL 41582 strain, it was previously demonstrated that the blue colour of the medium turned to red before complete dye decolourisation. To better understand the phenomenon, this study carried out ABu62 biotransformation with five different WRF strains (Coriolopsis polyzona MUCL 38443, Perenniporia ochroleuca MUCL 41114, Perenniporia tephropora MUCL 41562, P. sanguineus MUCL 38531 and Trametes versicolor MUCL 38412) and compared with P. sanguineus MUCL 41582 previously described. A multi-methodological approach (using capillary electrophoresis, mass spectrometry, HPLC, UV, NMR and IR spectroscopies) was developed to characterise the metabolites involved and monitor their apparition. Seven metabolites were commonly found with all strains, suggesting a common metabolic pathway for ABu62 biotransformation. During the first days, dimer and oligomers of the initial ABu62 molecule were observed: the main one absorbed in the 500nm region, explaining the red colour appearance of the medium. This main metabolite was made up of two molecules of ABu62 linked by an azo bond, minus a cyclohexyl moiety. After a longer incubation time, breakdown products were observed. Based on these products characterizations, a bioconversion pathway was proposed.

DyP, a unique dye-decolorizing peroxidase, represents a novel heme peroxidase family: ASP171 replaces the distal histidine of classical peroxidases

DyP, a unique dye-decolorizing enzyme from the fungus Thanatephorus cucumeris Dec 1, has been classified as a peroxidase but lacks homology to almost all other known plant peroxidases. The primary structure of DyP shows moderate sequence homology to only two known proteins: the peroxide-dependent phenol oxidase, TAP, and the hypothetical peroxidase, cpop21. Here, we show the first crystal structure of DyP and reveal that this protein has a unique tertiary structure with a distal heme region that differs from that of most other peroxidases. DyP lacks an important histidine residue known to assist in the formation of a Fe4+ oxoferryl center and a porphyrin-based cation radical intermediate (compound I) during the action of ubiquitous peroxidases. Instead, our tertiary structural and spectrophotometric analyses of DyP suggest that an aspartic acid and an arginine are involved in the formation of compound I. Sequence analysis reveals that the important aspartic acid and arginine mentioned above and histidine of the heme ligand are conserved among DyP, TAP, and cpop21, and structural and phylogenetic analyses confirmed that these three enzymes do not belong to any other families of peroxidase. These findings, which strongly suggest that DyP is a representative heme peroxidase from a novel family, should facilitate the identification of additional new family members and accelerate the classification of this novel peroxidase family.