Peroxidases-based enticing biotechnological platforms for biodegradation and biotransformation of emerging contaminants

Exploring Novel Fungal-Bacterial Consortia for Enhanced Petroleum Hydrocarbon Degradation

Bioremediation, involving the strategic use of microorganisms, has proven to be a cost-effective alternative for restoring areas impacted by persistent contaminants such as polycyclic aromatic hydrocarbons (PAHs). In this context, the aim of this study was to explore hydrocarbon-degrading microbial consortia by prospecting native species from soils contaminated with blends of diesel and biodiesel (20% biodiesel/80% diesel). After enrichment in a minimal medium containing diesel oil as the sole carbon source and based on 16S rRNA, Calmodulin and β-tubulin gene sequencing, seven fungi and 12 bacteria were identified. The drop collapse test indicated that all fungal and four bacterial strains were capable of producing biosurfactants with a surface tension reduction of ≥20%. Quantitative analysis of extracellular laccase production revealed superior enzyme activity among the bacterial strains, particularly for Stenotrophomonas maltophilia P05R11. Following antagonistic testing, four compatible consortia were formulated. The degradation analysis of PAHs and TPH (C5-C40) present in diesel oil revealed a significantly higher degradation capacity for the consortia compared to isolated strains. The best results were observed for a mixed bacterial-fungal consortium, composed of Trichoderma koningiopsis P05R2, Serratia marcescens P10R19 and Burkholderia cepacia P05R9, with a degradation spectrum of ≥91% for all eleven PAHs analyzed, removing 93.61% of total PAHs, and 93.52% of TPH (C5-C40). Furthermore, this study presents the first report of T. koningiopsis as a candidate for bioremediation of petroleum hydrocarbons.

Evaluating the estrogen degradation potential of laccase and peroxidase from Bacillus ligniniphilus L1 through integrated computational and experimental approaches

This study investigated the degradation potential of laccase and catalase-peroxidase from the extremophilic marine bacterium Bacillus ligniniphilus L1 against endogenous and synthetic estrogen compounds using an integrated computational and experimental approach. Molecular docking identified five estrogen compounds exhibiting reliable bindings with enzymes, which were then subjected to enzyme activity assays. The degradation potential of the two enzymes against five selected estrogen compounds were investigated and compared with their commercial counterparts. Laccase from L1 showed higher degradation potential against estrone (47.02 % without and 62.21 % with ABTS) compared to commercial laccase (39 % without and 54.20 % with ABTS). For estradiol valerate, commercial laccase showed a slightly higher degradation (52.47 %) than L1 laccase (49.94 %), but with ABTS, L1 laccase performed better (74.15 % vs. 68.03 %). Notably, L1 catalase-peroxidase demonstrated significantly higher degradation for all tested compounds compared to its commercial counterpart with efficiencies of 96.16 %, 89.09 %, 74.94 %, 64.91 %, and 62.80 % against estropipate, quinestrol, estradiol valerate, estriol and estrone, respectively, revealing its potential for commercial applications. Molecular dynamics simulations revealed the interaction and stability of enzyme-estrogen complexes, with MMGBSA binding energy calculations supporting experimental results. These findings highlight the usefulness of the computational approach in elucidating the molecular mechanisms underlying enzyme-mediated bioremediation of environmental contaminants.

Enzyme-Immobilized Porous Crystals for Environmental Applications

Developing efficient technologies to eliminate or degrade contaminants is paramount for environmental protection. Biocatalytic decontamination offers distinct advantages in terms of selectivity and efficiency; however, it still remains challenging when applied in complex environmental matrices. The main challenge originates from the instability and difficult-to-separate attributes of fragile enzymes, which also results in issues of compromised activity, poor reusability, low cost-effectiveness, etc. One viable solution to harness biocatalysis in complex environments is known as enzyme immobilization, where a flexible enzyme is tightly fixed in a solid carrier. In the case where a reticular crystal is utilized as the support, it is feasible to engineer next-generation biohybrid catalysts functional in complicated environmental media. This can be interpreted by three aspects: (1) the highly crystalline skeleton can shield the immobilized enzyme against external stressors. (2) The porous network ensures the high accessibility of the interior enzyme for catalytic decontamination. And (3) the adjustable and unambiguous structure of the reticular framework favors in-depth understanding of the interfacial interaction between the framework and enzyme, which can in turn guide us in designing highly active biocomposites. This Review aims to introduce this emerging biocatalysis technology for environmental decontamination involving pollutant degradation and greenhouse gas (carbon dioxide) conversion, with emphasis on the enzyme immobilization protocols and diverse catalysis principles including single enzyme catalysis, catalysis involving enzyme cascades, and photoenzyme-coupled catalysis. Additionally, the remaining challenges and forward-looking directions in this field are discussed. We believe that this Review may offer a useful biocatalytic technology to contribute to environmental decontamination in a green and sustainable manner and will inspire more researchers at the intersection of the environment science, biochemistry, and materials science communities to co-solve environmental problems.

Enzyme-immobilized hierarchically porous covalent organic framework biocomposite for catalytic degradation of broad-range emerging pollutants in water

Efficient enzyme immobilization is crucial for the successful commercialization of large-scale enzymatic water treatment. However, issues such as lack of high enzyme loading coupled with enzyme leaching present challenges for the widespread adoption of immobilized enzyme systems. The present study describes the development and bioremediation application of an enzyme biocomposite employing a cationic macrocycle-based covalent organic framework (COF) with hierarchical porosity for the immobilization of horseradish peroxidase (HRP). The intrinsic hierarchical porous features of the azacalix[4]arene-based COF (ACA-COF) allowed for a maximum HRP loading capacity of 0.76 mg/mg COF with low enzyme leaching (<5.0 %). The biocomposite, HRP@ACA-COF, exhibited exceptional thermal stability (∼200 % higher relative activity than the free enzyme), and maintained ∼60 % enzyme activity after five cycles. LCMSMS analyses confirmed that the HRP@ACA-COF system was able to achieve > 99 % degradation of seven diverse types of emerging pollutants (2-mercaptobenzothiazole, paracetamol, caffeic acid, methylparaben, furosemide, sulfamethoxazole, and salicylic acid)in under an hour. The described enzyme-COF system offers promise for efficient wastewater bioremediation applications.

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.

Electrochemical transformations catalyzed by cytochrome P450s and peroxidases

Cytochrome P450s (Cyt P450s) and peroxidases are enzymes featuring iron heme cofactors that have wide applicability as biocatalysts in chemical syntheses. Cyt P450s are a family of monooxygenases that oxidize fatty acids, steroids, and xenobiotics, synthesize hormones, and convert drugs and other chemicals to metabolites. Peroxidases are involved in breaking down hydrogen peroxide and can oxidize organic compounds during this process. Both heme-containing enzymes utilize active Fe^IVO intermediates to oxidize reactants. By incorporating these enzymes in stable thin films on electrodes, Cyt P450s and peroxidases can accept electrons from an electrode, albeit by different mechanisms, and catalyze organic transformations in a feasible and cost-effective way. This is an advantageous approach, often called bioelectrocatalysis, compared to their biological pathways in solution that require expensive biochemical reductants such as NADPH or additional enzymes to recycle NADPH for Cyt P450s. Bioelectrocatalysis also serves as an ex situ platform to investigate metabolism of drugs and bio-relevant chemicals. In this paper we review biocatalytic electrochemical reactions using Cyt P450s including C-H activation, S-oxidation, epoxidation, N-hydroxylation, and oxidative N-, and O-dealkylation; as well as reactions catalyzed by peroxidases including synthetically important oxidations of organic compounds. Design aspects of these bioelectrocatalytic reactions are presented and discussed, including enzyme film formation on electrodes, temperature, pH, solvents, and activation of the enzymes. Finally, we discuss challenges and future perspective of these two important bioelectrocatalytic systems.

Recent Advances in the Biocatalytic Mitigation of Emerging Pollutants: A Comprehensive Review

The issue of environmental pollution has been worsened by the emergence of new contaminants whose morphology is yet to be fully understood. Several techniques have been adopted to mitigate the pollution effects of these emerging contaminants, and bioremediation involving plants, microbes, or enzymes has stood out as a cost-effective and eco-friendly approach. Enzyme-mediated bioremediation is a very promising technology as it exhibits better pollutant degradation activity and generates less waste. However, this technology is subject to challenges like temperature, pH, and storage stability, in addition to recycling difficulty as it is arduous to isolate them from the reaction media. To address these challenges, the immobilization of enzymes has been successfully applied to ameliorate the activity, stability, and reusability of enzymes. Although this has significantly increased the uses of enzymes over a wide range of environmental conditions and facilitated the use of smaller bioreactors thereby saving cost, it still comes with additional costs for carriers and immobilization. Additionally, the existing immobilization methods have their individual limitations. This review provides state-of-the-art information to readers focusing on bioremediation using enzymes. Different parameters such as: the sustainability of biocatalysts, the ecotoxicological evaluation of transformation contaminants, and enzyme groups used were reviewed. The efficacy of free and immobilized enzymes, materials and methods for immobilization, bioreactors used, challenges to large-scale implementation, and future research needs were thoroughly discussed.

Bioremoval and Detoxification of the Anticancer Drug Mitoxantrone Using Immobilized Crude Versatile Peroxidase (icVP/Ba) Bjerkandera adusta CCBAS 930

The aim of this study was to evaluate the biodecolorization and detoxification of the anticancer drug mitoxantron (MTX) by immobilized crude versatile peroxidase of Bjerkandera adusta CCBAS 930 (icVP/Ba). The concentrated crude VP was obtained from B. adusta CCBAS 930 culture on medium with MTX (µg/mL) addition, immobilized with 4% sodium alginate. MTX removal degree (decolorization), levels of phenolic compounds and free radicals were determined during MTX biotransformation. Moreover, the phytotoxicity (Lepidium sativum L.), biotoxicity (multi-species microbial assay, MARA), and genotoxicity (SOS Chromotest) of MTX were evaluated before and after the biological treatment. The use of icVP/Ba (95 U/mL) significantly shortened the bioremoval of 10 µg/mL MTX (95.57% after 72 h). MTX removal by icVP/Ba was correlated with an 85% and 90% decrease in the levels of phenolic compounds and free radicals, respectively. In addition, the use of icVP/Ba contributed to a decrease in the phyto-, bio-, and genotoxicity of MTX. This is the first study to describe the possibility of removing MTX using immobilized crude fungal peroxidase.