Molecular dynamics study of biodegradation of azo dyes via their interactions with AzrC azoreductase

Omics-Based Approaches in Research on Textile Dye Microbial Decolorization

The development of the textile industry has negative effects on the natural environment. Cotton cultivation, dyeing fabrics, washing, and finishing require a lot of water and energy and use many chemicals. One of the most dangerous pollutants generated by the textile industry is dyes. Most of them are characterized by a complex chemical structure and an unfavorable impact on the environment. Especially azo dyes, whose decomposition by bacteria may lead to the formation of carcinogenic aromatic amines and raise a lot of concern. Using the metabolic potential of microorganisms that biodegrade dyes seems to be a promising solution for their elimination from contaminated environments. The development of omics sciences such as genomics, transcriptomics, proteomics, and metabolomics has allowed for a comprehensive approach to the processes occurring in cells. Especially multi-omics, which combines data from different biomolecular levels, providing an integrative understanding of the whole biodegradation process. Thanks to this, it is possible to elucidate the molecular basis of the mechanisms of dye biodegradation and to develop effective methods of bioremediation of dye-contaminated environments.

Revealing the degrading-possibility of methyl red by two azoreductases of Anoxybacillus sp. PDR2 based on molecular docking

Azo dyes, as the most widely used synthetic dyes, are considered to be one of the culprits of water resources and environmental pollution. Anoxybacillus sp. PDR2 is a thermophilic bacterium with the ability to degrade azo dyes, whose genome contains two genes encoding azoreductases (named AzoPDR2-1 and AzoPDR2-2). In this study, through response surface methodology (RSM), when the initial pH, inoculation volume and Mg2+ addition amount were 7.18, 10.72% and 0.1 g/L respectively, the decolorization rate of methyl red (MR) (200 mg/L) could reach its maximum (98.8%). The metabolites after biodegradation were detected by UV-Vis spectroscopy, Fourier transform infrared spectroscopy (FTIR), and liquid chromatography mass spectrometry (LC-MS/MS), indicating that MR was successfully decomposed into 4-aminobenzoic acid and other small substrates. In homologous modeling, it was found that both azoreductases were flavin-dependent azoreductases, and belonged to the α/β structure, using the Rossmann fold. In their docking results with the cofactor flavin mononucleotide (FMN), FMN bound to the surface of the protein dimer. Nicotinamide adenine dinucleotide (NADH) was superimposed on the plane of the pyrazine ring between FMN and the activity pocket of protein. Besides, both azoreductase complexes (azoreductase-FMN-NADH) exhibited a substrate preference for MR. Asn104 and Tyr74 played an important role in the combination of the azoreductase AzoPDR2-1 complex and the azoreductase AzoPDR2-2 complex with MR, respectively. This provided assistance for studying the mechanism of azoreductase biodegradation of azo dyes in thermophilic bacteria.

Exploring the role of microbial proteins in controlling environmental pollutants based on molecular simulation

Molecular simulation has been widely used to study microbial proteins' structural composition and dynamic properties, such as volatility, flexibility, and stability at the microscopic scale. Herein, this review describes the key elements of molecular docking and molecular dynamics (MD) simulations in molecular simulation; reviews the techniques combined with molecular simulation, such as crystallography, spectroscopy, molecular biology, and machine learning, to validate simulation results and bridge information gaps in the structure, microenvironmental changes, expression mechanisms, and intensity quantification; illustrates the application of molecular simulation, in characterizing the molecular mechanisms of interaction of microbial proteins with four different types of contaminants, namely heavy metals (HMs), pesticides, dyes and emerging contaminants (ECs). Finally, the review outlines the important role of molecular simulations in the study of microbial proteins for controlling environmental contamination and provides ideas for the application of molecular simulation in screening microbial proteins and incorporating targeted mutagenesis to obtain more effective contaminant control proteins.

Understanding the biodegradation pathways of azo dyes by immobilized white-rot fungus, Trametes hirsuta D7, using UPLC-PDA-FTICR MS supported by in silico simulations and toxicity assessment

No biodegradation methods are absolute in the treatment of all textile dyes, which leads to structure-dependent degradation. In this study, biodegradation of three azo dyes, reactive black 5 (RB5), acid blue 113 (AB113), and acid orange 7 (AO7), was investigated using an immobilized fungus, Trametes hirsuta D7. The degraded metabolites were identified using UPLC-PDA-FTICR MS and the biodegradation pathway followed was proposed. RB5 (92%) and AB113 (97%) were effectively degraded, whereas only 30% of AO7 was degraded. Molecular docking simulations were performed to determine the reason behind the poor degradation of AO7. Weak binding affinity, deficiency in H-bonding interactions, and the absence of interactions between the azo (-NN-) group and active residues of the model laccase enzyme were responsible for the low degradation efficiency of AO7. Furthermore, cytotoxicity and genotoxicity assays confirmed that the fungus-treated dye produced non-toxic metabolites. The observations of this study will be useful for understanding and further improving enzymatic dye biodegradation.

Biological Degradation of the Azo Dye Basic Orange 2 by Escherichia coli: A Sustainable and Ecofriendly Approach for the Treatment of Textile Wastewater

In this study, initially 11 different bacterial strains were tested for the degradation capabilities against Basic Orange 2 dye. In initial screening with 78.90% degradation activity, Escherichia coli emerged as the most promising strain to degrade the selected dye, and was then employed in subsequent experiments. For further enhancing the degradation capability of selected bacteria, the effects of various physicochemical parameters were also evaluated. Among the tested parameters, 20 ppm dye concentration, 1666 mg/L glucose concentration, a temperature of 40 °C, 666 mg/L sodium chloride concentration, pH 7, 1000 mg/L urea concentration, a 3-day incubation period and the use of sodium benzoate as a redox mediator (666 mg/L) were found to be ideal conditions to get the highest decolorization/degradation activities. Finally, all the mentioned parameters were combined in a single set of experiments, and the decolorization capacity of the bacteria was enhanced to 89.88%. The effect of pH, dye concentration, incubation time and temperature were found to be responsible for the optimum degradation of dye (p < 0.05), as predicted from the ANOVA (analysis of variance) of the response surface methodology. The metabolites were collected after completion of the process and characterized through Fourier transform irradiation (FTIR) and gas chromatography mass spectrometry (GC-MS). From the data obtained, a proposed mechanism was deduced where it was assumed that the azo bond of the dye was broken by the azoreductase enzyme of the bacteria, resulting in the formation of aniline and 3, 4-diaminobezeminium chloride. The aniline was then further converted to benzene by deamination by the action of the bacterial deaminase enzyme. The benzene ring, after subsequent methylation, was transformed into o-xylene, while 3, 4-diaminobezeminium chloride was converted to p-xylene by enzymatic action. These findings suggest that Escherichia coli is a capable strain to be used in the bioremediation of textile effluents containing azo dyes. However, the selected bacterial strain may need to be further investigated for other dyes as well.

Degradation of Azo Dyes: Bacterial Potential for Bioremediation

The use of dyes dates to ancient times and has increased due to population and industrial growth, leading to the rise of synthetic dyes. These pollutants are of great environmental impact and azo dyes deserve special attention due their widespread use and challenging degradation. Among the biological solutions developed to mitigate this issue, bacteria are highlighted for being versatile organisms, which can be applied as single organism cultures, microbial consortia, in bioreactors, acting in the detoxification of azo dyes breakage by-products and have the potential to combine biodegradation with the production of products of economic interest. These characteristics go hand in hand with the ability of various strains to act under various chemical and physical parameters, such as a wide range of pH, salinity, and temperature, with good performance under industry, and environmental, relevant conditions. This review encompasses studies with promising results related to the use of bacteria in the bioremediation of environments contaminated with azo dyes in the most diverse techniques and parameters, both in environmental and laboratory samples, also addressing their mechanisms and the legislation involving these dyes around the world, showcasing the importance of bacterial bioremediation, specialty in a scenario in an ever-increasing pursuit for sustainable production.

Augmented Biodegradation of Textile Azo Dye Effluents by Plant Endophytes: A Sustainable, Eco-Friendly Alternative

Textile industry consumes a large proportion of available water and releases huge amounts of toxic azo dye effluents, leading to an inevitable situation of acute environmental pollution that has been a significant threat to mankind. Decolorization or detoxification of harmful azo dyes has become a global priority to overcome the disastrous consequences and salvage the ecosystem. Biodegradation of textile azo dyes by endophytes stands to be a lucrative and viable alternative over conventional physico-chemical methods, owing to their eco-friendliness, cost-competitive and non-toxic nature. Especially, plant endophytic microbes exhibit promising biodegradation potential which has wired up the effective removal of textile azo dyes, attributing to their ability to produce dye degrading enzymes, laccases, peroxidases and azoreductases. Although both bacterial and fungal endophytes have been tried for azo dye degradation, endophytic fungi find broader application over bacteria. Despite of the advancements made in microbe-mediated biodegradation, there is still a need to fill the gap in lab to in situ translation of biodegradation research. This review concisely accentuates the xenobiotics of textile azo dyes and microbial mechanisms of biodegradation of textile azo dyes, positing plant endophytic community, especially bacterial and fungal endophytes as the potential dye degraders, highlighting currently reported dye degrading endophytic species.

Application of docking and active site analysis for enzyme linked biodegradation of textile dyes

Growth of textile industries led to production of enormous dye varieties. These textile dyes are largely used, chemically stable and easy to synthesize. But they are recalcitrant and persist as less biodegradable pollutants when discharged into waterbodies. Potential use of enzyme-linked bioremediation of textile dyes will control their toxicity in waterbodies. Bioinformatics and Molecular docking tool provides an insight into remediation mechanism by predicting susceptibility of dye degradation using oxidoreductive enzymes. In this study, six dyes, Reactive Red F3B, Remazol Red RGB, Joyfix Red RB, Joyfix Yellow MR, Remazol Blue RGB and Turquoise CL-5B of azo, anthraquinone and phthalocyanine molecular class were identified as potential targets for degradation by laccase and azoreductase of Aeromonas hydrophila in addition to Lysinibacillus sphaericus through in silico docking tool BioSolveIT-FlexX. Azoreductase breaks azo bonds by ping-pong mechanism whereas laccase decolorizes dyes by free radical mechanism which is not specific in nature. Results were analyzed based on parameters like stability, catalytic action and selectivity for enzyme-dye interactions. Amino acids of enzymes interacted with several dyes substantiating variations in active site for enzyme-ligand binding affinity. This suggests the role of enzymes in decolorizing an extensive variety of textile dyes, thereby, aiding in understanding the enzyme mechanisms in Bioremediation.

Recent Developments and Applications of the MMPBSA Method

The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach has been widely applied as an efficient and reliable free energy simulation method to model molecular recognition, such as for protein-ligand binding interactions. In this review, we focus on recent developments and applications of the MMPBSA method. The methodology review covers solvation terms, the entropy term, extensions to membrane proteins and high-speed screening, and new automation toolkits. Recent applications in various important biomedical and chemical fields are also reviewed. We conclude with a few future directions aimed at making MMPBSA a more robust and efficient method.