Elucidation of fungal dye-decolourizing peroxidase (DyP) and ligninolytic enzyme activities in decolourization and mineralization of azo dyes

Robust peroxidase from Bacillus mojavensis TH309: Immobilization on walnut shell hydrochar and evaluation of its potential in dye decolorization

Peroxidases have received considerable attention as a cost-effective and environmentally friendly catalyst for bioremediation. Their rapid activity loss under harsh environmental conditions and inability to be used repetitively limit their exploitation in real-world wastewater treatment. First, a peroxidase was produced extracellularly by Bacillus mojavensis TH309 and purified 8.12-fold with a final yield of 47.10 % using Sephadex G-100 superfine resin. The pure peroxidase (BmPer) possessed a relatively low molecular weight of ∼21 kDa and was active against L-DOPA on acrylamide gel after electrophoresis. BmPer was immobilized by adsorption functionalized walnut shell hydrochar (WsH) with 61.99 ± 1.34 % efficiency and 37.07 ± 4.16 % activity loss. BmPer and its immobilized form (WsH-BmPer) exhibited maximum activity at 50 °C and pH 9. WsH-BmPer exhibited 3.23-, 2.37-, 1.65-, and 2.25-fold longer half-life than BmPer at 50, 60, 70, and 80 °C, respectively. Immobilization significantly enhanced the stability of the enzyme under acidic conditions. BmPer and WsH-BmPer showed maximal activity in the presence of 1 % salt and retained more than 85 % of their activity even after pre-incubation with 2.5 M salt for 60 min at 50 °C. Their catalytic efficiency was significantly stimulated by pre-incubation with Triton X-100 (1 mM), Tween20 (1 mM), and Mg2+ (1 and 10 mM). Immobilization strongly reduced the loss of activity caused by inhibitors including Ba2+, Hg2+, and Cu2+. Moreover, both forms of the enzyme were compatible with solvents. The Michaelis constant (Km) values of BmPer and WsH-BmPer were 0.88 and 2.66 mM for 2,4 DCP, respectively. WsH-BmPer peroxidase maintained about 82 % and 85 % of its activity when stored at 4 °C for 30 days and reused for up to 10 cycles, respectively. Furthermore, it decolorized Cibacron red (CR), Poly R-478 (PR), Remazol Brilliant Blue R (RBBR), and Methyl red (MR) dyes by 60.13 %, 91.34 %, 86.41 %, and 50.51 % within 60 min, respectively.

Heterologous expression, purification and structural features of native Dictyostelium discoideum dye-decolorizing peroxidase bound to a natively incorporated heme

The Dictyostelium discoideum dye-decolorizing peroxidase (DdDyP) is a newly discovered peroxidase, which belongs to a unique class of heme peroxidase family that lacks homology to the known members of plant peroxidase superfamily. DdDyP catalyzes the H2O2-dependent oxidation of a wide-spectrum of substrates ranging from polycyclic dyes to lignin biomass, holding promise for potential industrial and biotechnological applications. To study the molecular mechanism of DdDyP, highly pure and functional protein with a natively incorporated heme is required, however, obtaining a functional DyP-type peroxidase with a natively bound heme is challenging and often requires addition of expensive biosynthesis precursors. Alternatively, a heme in vitro reconstitution approach followed by a chromatographic purification step to remove the excess heme is often used. Here, we show that expressing the DdDyP peroxidase in ×2 YT enriched medium at low temperature (20°C), without adding heme supplement or biosynthetic precursors, allows for a correct native incorporation of heme into the apo-protein, giving rise to a stable protein with a strong Soret peak at 402 nm. Further, we crystallized and determined the native structure of DdDyP at a resolution of 1.95 Å, which verifies the correct heme binding and its geometry. The structural analysis also reveals a binding of two water molecules at the distal site of heme plane bridging the catalytic residues (Arg239 and Asp149) of the GXXDG motif to the heme-Fe(III) via hydrogen bonds. Our results provide new insights into the geometry of native DdDyP active site and its implication on DyP catalysis.

Heterogeneous biocatalytic system for effective decolorization of textile dye effluent

The current physicochemical methods for decolorizing toxic synthetic dyes are not sustainable to halt the environmental damage as they are expensive and often produce concentrated sludge, which may lead to secondary disposal problems. Biocatalysis (microbes and/or their enzymes) is a cost-effective, versatile, energy-saving and clean alternative. The most common enzymes involved in dye degradation are laccases, azoreductases and peroxidases. Toxic dyes could be converted into less harmful byproducts through the combined action of many enzymes or the utilization of whole cells. The action of whole cells to treat dye effluents is either by biosorption or degradation (aerobic or anaerobic). Using immobilized cells or enzymes will offer advantages such as superior stability, persistence against harsh environmental conditions, reusability and longer half-lives. This review envisages the recent strategies of immobilization and bioreactor considerations with the immobilized system as the effective treatment of textile dye effluents. Packed bed reactors are the most popular heterogeneous biocatalytic reactors for dye decolorization due to their efficiency and cost-effectiveness.

Genomic Diversity and Phenotypic Variation in Fungal Decomposers Involved in Bioremediation of Persistent Organic Pollutants

Fungi work as decomposers to break down organic carbon, deposit recalcitrant carbon, and transform other elements such as nitrogen. The decomposition of biomass is a key function of wood-decaying basidiomycetes and ascomycetes, which have the potential for the bioremediation of hazardous chemicals present in the environment. Due to their adaptation to different environments, fungal strains have a diverse set of phenotypic traits. This study evaluated 320 basidiomycetes isolates across 74 species for their rate and efficiency of degrading organic dye. We found that dye-decolorization capacity varies among and within species. Among the top rapid dye-decolorizing fungi isolates, we further performed genome-wide gene family analysis and investigated the genomic mechanism for their most capable dye-degradation capacity. Class II peroxidase and DyP-type peroxidase were enriched in the fast-decomposer genomes. Gene families including lignin decomposition genes, reduction-oxidation genes, hydrophobin, and secreted peptidases were expanded in the fast-decomposer species. This work provides new insights into persistent organic pollutant removal by fungal isolates at both phenotypic and genotypic levels.

Light driven Aspergillus niger-ZnS nanobiohybrids for degradation of methyl orange

Inorganic-microbial hybrid systems have potential to be sustainable, efficient and versatile chemical synthesis platforms by integrating the light-harvesting properties of semiconductors with microbial cells. Here, we demonstrate light-driven photocatalytic semiconducting Aspergillus niger cells-ZnS nanoparticles for enhanced removal of the dye methyl orange. Chemically synthesized ZnS nanoparticles exhibited a zinc blende pattern in X-ray diffraction, had a dimension of 20-90 nm with a band gap (E_bg) of 3.4 eV at 1.83 × 10¹⁸ photons/second. Biologically synthesized ZnS nanoparticles of 40-90 nm showed a hexagonal pattern in the X-ray powder diffraction spectra with an E_bg 3.7 eV at 1.68 × 10¹⁸ photons/second. At a methyl orange (MO) concentration of 100 mg/L, dosage of 0.5 × 10⁵ mol catalyst and pH 4, a 97.5% and 98% removal efficiency of MO was achieved in 90 min and 60 min for, respectively, chemically and biologically synthesized ZnS nanobiohybrids in the presence of UV-A light. The major degradation products of photocatalysis for chemically synthesized ZnS nanobiohybrids were naphtholate (C₁₀H₇O m/z 143) and hydroquinone (C₉H₅m/z 113). For the biologically synthesized ZnS nanobiohybrids, the degradation products were hydroquinone (C₉H₅m/z 113) and 2-phenylphenol (C₁₂H₁₀O m/z 170).

Efficient degradation of various emerging pollutants by wild type and evolved fungal DyP4 peroxidases

The accumulation of emerging pollutants in the environment remains a major concern as evidenced by the increasing number of reports citing their potential risk on environment and health. Hence, removal strategies of such pollutants remain an active area of investigation. One way through which emerging pollutants can be eliminated from the environment is by enzyme-mediated bioremediation. Enzyme-based degradation can be further enhanced via advanced protein engineering approaches. In the present study a sensitive and robust bioanalytical liquid chromatography-tandem mass spectrometry (LCMSMS)-based approach was used to investigate the ability of a fungal dye decolorizing peroxidase 4 (DyP4) and two of its evolved variants—that were previously shown to be H₂O₂ tolerant—to degrade a panel of 15 different emerging pollutants. Additionally, the role of a redox mediator was examined in these enzymatic degradation reactions. Our results show that three emerging pollutants (2-mercaptobenzothiazole (MBT), paracetamol, and furosemide) were efficiently degraded by DyP4. Addition of the redox mediator had a synergistic effect as it enabled complete degradation of three more emerging pollutants (methyl paraben, sulfamethoxazole and salicylic acid) and dramatically reduced the time needed for the complete degradation of MBT, paracetamol, and furosemide. Further investigation was carried out using pure MBT to study its degradation by DyP4. Five potential transformation products were generated during the enzymatic degradation of MBT, which were previously reported to be produced during different bioremediation approaches. The current study provides the first instance of the application of fungal DyP4 peroxidases in bioremediation of emerging pollutants.

A Comprehensive Insight into Fungal Enzymes: Structure, Classification, and Their Role in Mankind's Challenges

Enzymes have played a crucial role in mankind's challenges to use different types of biological systems for a diversity of applications. They are proteins that break down and convert complicated compounds to produce simple products. Fungal enzymes are compatible, efficient, and proper products for many uses in medicinal requests, industrial processing, bioremediation purposes, and agricultural applications. Fungal enzymes have appropriate stability to give manufactured products suitable shelf life, affordable cost, and approved demands. Fungal enzymes have been used from ancient times to today in many industries, including baking, brewing, cheese making, antibiotics production, and commodities manufacturing, such as linen and leather. Furthermore, they also are used in other fields such as paper production, detergent, the textile industry, and in drinks and food technology in products manufacturing ranging from tea and coffee to fruit juice and wine. Recently, fungi have been used for the production of more than 50% of the needed enzymes. Fungi can produce different types of enzymes extracellularly, which gives a great chance for producing in large amounts with low cost and easy viability in purified forms using simple purification methods. In the present review, a comprehensive trial has been advanced to elaborate on the different types and structures of fungal enzymes as well as the current status of the uses of fungal enzymes in various applications.

Dye Decoloring Peroxidase Structure, Catalytic Properties and Applications: Current Advancement and Futurity

Dye decoloring peroxidases (DyPs) were named after their high efficiency to decolorize and degrade a wide range of dyes. DyPs are a type of heme peroxidase and are quite different from known heme peroxidases in terms of amino acid sequences, protein structure, catalytic residues, and physical and chemical properties. DyPs oxidize polycyclic dyes and phenolic compounds. Thus they find high application potentials in dealing with environmental problems. The structure and catalytic characteristics of DyPs of different families from the amino acid sequence, protein structure, and enzymatic properties, and analyzes the high-efficiency degradation ability of some DyPs in dye and lignin degradation, which vary greatly among DyPs classes. In addition, application prospects of DyPs in biomedicine and other fields are also discussed briefly. At the same time, the research strategy based on genetic engineering and synthetic biology in improving the stability and catalytic activity of DyPs are summarized along with the important industrial applications of DyPs and associated challenges. Moreover, according to the current research findings, bringing DyPs to the industrial level may require improving the catalytic efficiency of DyP, increasing production, and enhancing alkali resistance and toxicity.

Mycoremediation and toxicity assessment of textile effluent pertaining to its possible correlation with COD

Globally, textile industries are one of the major sectors releasing dye pollutants. This is the first report on the positive correlation between toxicity and chemical oxygen demand (COD) of textile effluent along with the proposed pathway for enzymatic degradation of acid orange 10 using Geotrichum candidum within a very short stretch of time (18 h). Removal efficiency of this mycoremedial approach after 18 h in terms of chemical oxygen demand, biological oxygen demand, total suspended solids, salinity, color and dye concentration in the treated effluent reached to 98.5%, 56.3%,73.2%, 64%, 89% and 87% respectively. Also there was a decrease in pH of the treated effluent. FTIR analysis of the treated effluent confirmed biodegradation. The LCMS analysis showed the degradation of acid orange 10, which was confirmed by the formation of two biodegradation products, 7-oxo-8-iminonapthalene-1,3-disulfonate and nitrosobenzene, which subsequently undergoes stepwise hydrogenation and dehydration to form aniline via phenyl hydroxyl amine as intermediate. The X-ray diffraction studies showed that heavy metal content in the treated effluent has reduced along with decrease in % crystallinity, indicating biodegradation. The connection between toxicity and COD was also inveterated using Pearson's correlation coefficient. Further the toxicological studies indicated the toxicity of raw textile effluent and relatively lower toxic nature of metabolites generated after biodegradation by G. candidum.

Evaluation of Peroxidase in Herbal Medicines Based on an Electrochemical Sensor

Peroxidases are species-specific. Differences in peroxidase can objectively reflect the genetics among species. The use of peroxidase to assist in species identification is relatively simple and effective. In this work, we proposed a graphene-modified electrode. This electrode can amplify the signal of electrocatalytic reduction of hydrogen peroxide. Since peroxidase can catalyze the reduction of hydrogen peroxide, this signal can be used as an indicator to demonstrate the content of peroxidase in different plant tissues. Twelve herbal medicines were selected for our study. The results show that this electrochemical-based detection technique was comparable to colorimetric method in terms of accuracy.