Microbial capacities drive waste stabilization and resource recovery in environmental friendly pr... more Microbial capacities drive waste stabilization and resource recovery in environmental friendly processes. Depending on the composition of waste, a stress-mediated selection process ensures a scenario that generates a specific enrichment of microbial community. These communities dynamically change over a period of time while keeping the performance through the required utilization capacities. Depending on the environmental conditions, these communities select the appropriate partners so as to maintain the desired functional capacities. However, the complexities of these organizations are difficult to study. Individual member ratios and sharing of genetic intelligence collectively decide the enrichment and survival of these communities. The next-generation sequencing options with the depth of structure and function analysis have emerged as a tool that could provide the finer details of the underlying bioprocesses associated and shared in environmental niches. These tools can help in identification of the key biochemical events and monitoring of expression of associated phenotypes that will support the operation and maintenance of waste management systems. In this chapter, we link genomic tools with process optimization and/or management, which could be applied for decision making and/or upscaling. This review describes both, the aerobic and anaerobic, options of waste utilization process with the microbial community functioning as flocs, granules, or biofilms. There are a number of challenges involved in harnessing the microbial community intelligence with associated functional plasticity for efficient extension of microbial capacities for resource recycling and waste management. Mismanaged wastes could lead to undesired genotypes such as antibiotic/multidrug-resistant microbes.
The study employs draft genome sequence data to explore p-nitrophenol (PNP) degradation activity ... more The study employs draft genome sequence data to explore p-nitrophenol (PNP) degradation activity of Pseudomonas putida strain SF-1 at a genomic scale. Annotation analysis proposes that the strain SF1 not only possesses the gene cluster for PNP utilization but also for the utilization of benzoate, catechol, hydroxybenzoate, protocatechuate, and homogentisate. Further, the analysis was carried out to understand more details of PNP 4-monooxygenase and its regulator. A comparative analysis of PNP 4-monooxygenase from SF1 was carried out for prediction of its tertiary structure; and also its binding affinity with PNP, FAD, NADH and NADPH using FlexX docking. The tertiary structure of regulator was also predicted along with its conserved DNA binding residues. Regulator binding site (RBS) and promoter region were mapped for the PNP degradation gene cluster. Based on genome sequence analysis, the study unveiled the genomic attributes for a versatile catabolic potential of Pseudomonas putida strain SF-1 for different aromatic compounds.
Microbial capacities drive waste stabilization and resource recovery in environmental friendly pr... more Microbial capacities drive waste stabilization and resource recovery in environmental friendly processes. Depending on the composition of waste, a stress-mediated selection process ensures a scenario that generates a specific enrichment of microbial community. These communities dynamically change over a period of time while keeping the performance through the required utilization capacities. Depending on the environmental conditions, these communities select the appropriate partners so as to maintain the desired functional capacities. However, the complexities of these organizations are difficult to study. Individual member ratios and sharing of genetic intelligence collectively decide the enrichment and survival of these communities. The next-generation sequencing options with the depth of structure and function analysis have emerged as a tool that could provide the finer details of the underlying bioprocesses associated and shared in environmental niches. These tools can help in identification of the key biochemical events and monitoring of expression of associated phenotypes that will support the operation and maintenance of waste management systems. In this chapter, we link genomic tools with process optimization and/or management, which could be applied for decision making and/or upscaling. This review describes both, the aerobic and anaerobic, options of waste utilization process with the microbial community functioning as flocs, granules, or biofilms. There are a number of challenges involved in harnessing the microbial community intelligence with associated functional plasticity for efficient extension of microbial capacities for resource recycling and waste management. Mismanaged wastes could lead to undesired genotypes such as antibiotic/multidrug-resistant microbes.
The study employs draft genome sequence data to explore p-nitrophenol (PNP) degradation activity ... more The study employs draft genome sequence data to explore p-nitrophenol (PNP) degradation activity of Pseudomonas putida strain SF-1 at a genomic scale. Annotation analysis proposes that the strain SF1 not only possesses the gene cluster for PNP utilization but also for the utilization of benzoate, catechol, hydroxybenzoate, protocatechuate, and homogentisate. Further, the analysis was carried out to understand more details of PNP 4-monooxygenase and its regulator. A comparative analysis of PNP 4-monooxygenase from SF1 was carried out for prediction of its tertiary structure; and also its binding affinity with PNP, FAD, NADH and NADPH using FlexX docking. The tertiary structure of regulator was also predicted along with its conserved DNA binding residues. Regulator binding site (RBS) and promoter region were mapped for the PNP degradation gene cluster. Based on genome sequence analysis, the study unveiled the genomic attributes for a versatile catabolic potential of Pseudomonas putida...
World Journal of Microbiology and Biotechnology, 2023
Abstract
Hydrophobic organic compounds, either natural or introduced through anthropogenic activ... more Abstract
Hydrophobic organic compounds, either natural or introduced through anthropogenic activities, pose a serious threat to all spheres of life, including humankind. These hydrophobic compounds are recalcitrant and difficult to degrade by the
microbial system; however, microbes have also evolved their metabolic and degradative potential. Pseudomonas species have been reported to have a multipotential role in the biodegradation of aromatic hydrocarbons through aromatic ringhydroxylating dioxygenases (ARHDs). The structural complexity of different hydrophobic substrates and their chemically inert nature demands the explicit role of evolutionary conserved multicomponent enzyme ARHDs. These enzymes
catalyze ring activation and subsequent oxidation by adding two molecular oxygen atoms onto the vicinal carbon of the aromatic nucleus. This critical metabolic step in the aerobic mode of degradation of polycyclic aromatic hydrocarbons (PAHs) catalyzed by ARHDs can also be explored through protein molecular docking studies. Protein data analysis enables an understanding of molecular processes and monitoring complex biodegradation reactions. This review summarizes the molecular characterization of five ARHDs from Pseudomonas species already reported for PAH degradation. Homology modeling for the amino acid sequences encoding the catalytic α-subunit of ARHDs and their docking analyses with PAHs suggested that the enzyme active sites show flexibility around the catalytic pocket for binding of low molecular
weight (LMW) and high molecular weight (HMW) PAH substrates (naphthalene, phenanthrene, pyrene, benzo[α]pyrene). The alpha subunit harbours variable catalytic pockets and broader channels, allowing relaxed enzyme specificity toward PAHs. ARHD’s ability to accommodate different LMW and HMW PAHs demonstrates its ‘plasticity’, meeting the catabolic demand of the PAH degraders
International Journal of Environmental Science and Technology
Bacterial cells dwelling in the Polycyclic Aromatic Hydrocarbons (PAH) contaminated ecosystem occ... more Bacterial cells dwelling in the Polycyclic Aromatic Hydrocarbons (PAH) contaminated ecosystem occur as an eco-community or biofilms having biosurfactants and exopolymeric substances (EPS) producing capacity. Bacteria have developed several mechanisms to utilize the low accessible PAH compounds by modifying their structural and physiological process. EPS provides an adsorption site for PAH binding and acts as an emulsifier, enhancing PAH uptake in bacterial cells. Biosurfactants aid in the solubilization of the low-bioavailable carbon sources by reducing the interfacial surface tension between the aqueous phase and PAH-sorbent matrix, solubilizing PAHs thus making them bioavailable. Mining of exopolysaccharides synthesizing key genes (priming Glycosyltransferase) and biosurfactant producing genes (synthetases) in PAH degrading bacteriomes established their concomitant involvement in PAH solubilization and uptake. The transcriptional and translational regulators (secondary messenger cyclic-di-GMP, quorum sensing molecules, small ribosomal RNAs, two-component signaling molecules) control the synthesis of these ‘bioavailability enhancers’ towards PAH utilization and have been elucidated explicitly in the current review.
provides habitats to microorganisms. Changes in soil properties, productivity, and, inevitably co... more provides habitats to microorganisms. Changes in soil properties, productivity, and, inevitably contamination/ stress are the result of urbanisation, industrialization, and long-term use of synthetic fertiliser. Therefore, in the recent scenario, reclamation of contaminated/stressed soils has become a potential challenge. Several customized, such as, physical, chemical, and biological technologies have been deployed so far to restore contaminated land. Among them, microbial-assisted phytoremediation is considered as an economical and greener approach. In recent decades, soil microbes have successfully been used to improve plants’ ability to tolerate biotic and abiotic stress and strengthen their phytoremediation capacity. Therefore, in this context, the current review work critically explored the microbial assisted phytoremediation mechanisms to restore different types of stressed soil. The role of plant growth-promoting rhizobacteria (PGPR) and their potential mechanisms that foster plants’ growth and also enhance phytoremediation capacity are focussed. Finally, this review has emphasized on the application of advanced tools and techniques to effectively characterize potent soil microbial communities and their significance in boosting the phytoremediation process of stressed soils along with prospects for future research.
The green synthesis of nanoparticles (NPs) is the safest, ecofriendly, cost-effective, and non-ha... more The green synthesis of nanoparticles (NPs) is the safest, ecofriendly, cost-effective, and non-hazardous approach of nanotechnology. In the current study, we described the green synthesis of silver nanoparticles (AgNPs) using Cuphea carthagenensis aqueous leaf extract as a reducing, capping, and stabilizing agent. The study aims at the synthesis, characterization, optimization, and determination of the antibacterial activity of Cc-AgNPs against clinically important human pathogens. Coating of cotton fabrics with Cc-AgNPs and their efficacy against skin infection causing organisms was also evaluated. Furthermore, antioxidant activity, growth assay and time kill assay of Cc-AgNPs were also performed in the study. The biosynthesized Cc-AgNPs were characterized by UV-visible spectrometry, energy-dispersive X-ray spectroscopy (EDX), X-ray diffraction (XRD), transmission electron microscopy (TEM), and Fourier transform infrared spectroscopy (FTIR). The spectroscopic and microscopic analysis demonstrated biosynthesis of face-centered cubic (fcc) crystalline spherical Cc-AgNPs with an average particle size of 10.65 ± 0.1 nm. Optimized peak synthesis of Cc-AgNPs was reported at pH7, 55 °C, 4 mM silver nitrate, and 5:45 (plant extract: silver nitrate). Cc-AgNPs exhibited potent antioxidant effect and antibacterial activity against both Gram-positive and Gram-negative bacteria. The lowest MIC (15 μg/ml) and MBC (25 μg/ml) values were reported against S. typhimurium. The Cc-AgNPs coated fabrics demonstrated potent antibacterial activity against tested strains. This application could be helpful in wound healing management. Furthermore, the hemolytic analysis demonstrated that Cc-AgNPs exhibit non-toxic nature against Red Blood Cells (RBCs) at the tested concentrations. In conclusion, the investigation demonstrated a fast, stable, and eco-friendly approach to the biosynthesis of Cc-AgNPs along with their antibacterial and antioxidant properties.
Optimization and Applicability of Bioprocesses, 2017
Biofilms are resilient and complex microbial communities or populations encased in a self-produci... more Biofilms are resilient and complex microbial communities or populations encased in a self-producing extracellular matrix existing in nature, which account for their robustness against a wide variety of stresses. In nature, multispecies biofilms have been found to occur frequently, whereas monospecies biofilms have been rare and found only when developed. By understanding the sociobiology of biofilm bacteria and harnessing the knowledge based on known biochemical and physical parameters, the underlying complexity of biofilm microenvironment could be better predicted by state-of-the-art advanced modeling approaches. In the present review, in-depth advanced modeling approaches based on the action of substrates on developmental biofilm physiology have been discussed. Equations for forces and adherence, quorum sensing, fluid flow dynamics, the social arrangement of community members in their favorable places, stratification, and pattern formation inside the biofilm have been elaborated. Equations to predict biofilm dispersal stages have been also discussed. Different models which uncover microbial biofilm life cycle stages to predict their complexity and recommended future variables like “omics” for magnification have been reported. This chapter will help to provide additional platform related to the genetic complex networking of biofilm bacteria for conceptual underpinnings of biofilm microenvironment.
Microbial capacities drive waste stabilization and resource recovery in environmental friendly pr... more Microbial capacities drive waste stabilization and resource recovery in environmental friendly processes. Depending on the composition of waste, a stress-mediated selection process ensures a scenario that generates a specific enrichment of microbial community. These communities dynamically change over a period of time while keeping the performance through the required utilization capacities. Depending on the environmental conditions, these communities select the appropriate partners so as to maintain the desired functional capacities. However, the complexities of these organizations are difficult to study. Individual member ratios and sharing of genetic intelligence collectively decide the enrichment and survival of these communities. The next-generation sequencing options with the depth of structure and function analysis have emerged as a tool that could provide the finer details of the underlying bioprocesses associated and shared in environmental niches. These tools can help in identification of the key biochemical events and monitoring of expression of associated phenotypes that will support the operation and maintenance of waste management systems. In this chapter, we link genomic tools with process optimization and/or management, which could be applied for decision making and/or upscaling. This review describes both, the aerobic and anaerobic, options of waste utilization process with the microbial community functioning as flocs, granules, or biofilms. There are a number of challenges involved in harnessing the microbial community intelligence with associated functional plasticity for efficient extension of microbial capacities for resource recycling and waste management. Mismanaged wastes could lead to undesired genotypes such as antibiotic/multidrug-resistant microbes.
The study employs draft genome sequence data to explore p-nitrophenol (PNP) degradation activity ... more The study employs draft genome sequence data to explore p-nitrophenol (PNP) degradation activity of Pseudomonas putida strain SF-1 at a genomic scale. Annotation analysis proposes that the strain SF1 not only possesses the gene cluster for PNP utilization but also for the utilization of benzoate, catechol, hydroxybenzoate, protocatechuate, and homogentisate. Further, the analysis was carried out to understand more details of PNP 4-monooxygenase and its regulator. A comparative analysis of PNP 4-monooxygenase from SF1 was carried out for prediction of its tertiary structure; and also its binding affinity with PNP, FAD, NADH and NADPH using FlexX docking. The tertiary structure of regulator was also predicted along with its conserved DNA binding residues. Regulator binding site (RBS) and promoter region were mapped for the PNP degradation gene cluster. Based on genome sequence analysis, the study unveiled the genomic attributes for a versatile catabolic potential of Pseudomonas putida strain SF-1 for different aromatic compounds.
Microbial capacities drive waste stabilization and resource recovery in environmental friendly pr... more Microbial capacities drive waste stabilization and resource recovery in environmental friendly processes. Depending on the composition of waste, a stress-mediated selection process ensures a scenario that generates a specific enrichment of microbial community. These communities dynamically change over a period of time while keeping the performance through the required utilization capacities. Depending on the environmental conditions, these communities select the appropriate partners so as to maintain the desired functional capacities. However, the complexities of these organizations are difficult to study. Individual member ratios and sharing of genetic intelligence collectively decide the enrichment and survival of these communities. The next-generation sequencing options with the depth of structure and function analysis have emerged as a tool that could provide the finer details of the underlying bioprocesses associated and shared in environmental niches. These tools can help in identification of the key biochemical events and monitoring of expression of associated phenotypes that will support the operation and maintenance of waste management systems. In this chapter, we link genomic tools with process optimization and/or management, which could be applied for decision making and/or upscaling. This review describes both, the aerobic and anaerobic, options of waste utilization process with the microbial community functioning as flocs, granules, or biofilms. There are a number of challenges involved in harnessing the microbial community intelligence with associated functional plasticity for efficient extension of microbial capacities for resource recycling and waste management. Mismanaged wastes could lead to undesired genotypes such as antibiotic/multidrug-resistant microbes.
The study employs draft genome sequence data to explore p-nitrophenol (PNP) degradation activity ... more The study employs draft genome sequence data to explore p-nitrophenol (PNP) degradation activity of Pseudomonas putida strain SF-1 at a genomic scale. Annotation analysis proposes that the strain SF1 not only possesses the gene cluster for PNP utilization but also for the utilization of benzoate, catechol, hydroxybenzoate, protocatechuate, and homogentisate. Further, the analysis was carried out to understand more details of PNP 4-monooxygenase and its regulator. A comparative analysis of PNP 4-monooxygenase from SF1 was carried out for prediction of its tertiary structure; and also its binding affinity with PNP, FAD, NADH and NADPH using FlexX docking. The tertiary structure of regulator was also predicted along with its conserved DNA binding residues. Regulator binding site (RBS) and promoter region were mapped for the PNP degradation gene cluster. Based on genome sequence analysis, the study unveiled the genomic attributes for a versatile catabolic potential of Pseudomonas putida...
World Journal of Microbiology and Biotechnology, 2023
Abstract
Hydrophobic organic compounds, either natural or introduced through anthropogenic activ... more Abstract
Hydrophobic organic compounds, either natural or introduced through anthropogenic activities, pose a serious threat to all spheres of life, including humankind. These hydrophobic compounds are recalcitrant and difficult to degrade by the
microbial system; however, microbes have also evolved their metabolic and degradative potential. Pseudomonas species have been reported to have a multipotential role in the biodegradation of aromatic hydrocarbons through aromatic ringhydroxylating dioxygenases (ARHDs). The structural complexity of different hydrophobic substrates and their chemically inert nature demands the explicit role of evolutionary conserved multicomponent enzyme ARHDs. These enzymes
catalyze ring activation and subsequent oxidation by adding two molecular oxygen atoms onto the vicinal carbon of the aromatic nucleus. This critical metabolic step in the aerobic mode of degradation of polycyclic aromatic hydrocarbons (PAHs) catalyzed by ARHDs can also be explored through protein molecular docking studies. Protein data analysis enables an understanding of molecular processes and monitoring complex biodegradation reactions. This review summarizes the molecular characterization of five ARHDs from Pseudomonas species already reported for PAH degradation. Homology modeling for the amino acid sequences encoding the catalytic α-subunit of ARHDs and their docking analyses with PAHs suggested that the enzyme active sites show flexibility around the catalytic pocket for binding of low molecular
weight (LMW) and high molecular weight (HMW) PAH substrates (naphthalene, phenanthrene, pyrene, benzo[α]pyrene). The alpha subunit harbours variable catalytic pockets and broader channels, allowing relaxed enzyme specificity toward PAHs. ARHD’s ability to accommodate different LMW and HMW PAHs demonstrates its ‘plasticity’, meeting the catabolic demand of the PAH degraders
International Journal of Environmental Science and Technology
Bacterial cells dwelling in the Polycyclic Aromatic Hydrocarbons (PAH) contaminated ecosystem occ... more Bacterial cells dwelling in the Polycyclic Aromatic Hydrocarbons (PAH) contaminated ecosystem occur as an eco-community or biofilms having biosurfactants and exopolymeric substances (EPS) producing capacity. Bacteria have developed several mechanisms to utilize the low accessible PAH compounds by modifying their structural and physiological process. EPS provides an adsorption site for PAH binding and acts as an emulsifier, enhancing PAH uptake in bacterial cells. Biosurfactants aid in the solubilization of the low-bioavailable carbon sources by reducing the interfacial surface tension between the aqueous phase and PAH-sorbent matrix, solubilizing PAHs thus making them bioavailable. Mining of exopolysaccharides synthesizing key genes (priming Glycosyltransferase) and biosurfactant producing genes (synthetases) in PAH degrading bacteriomes established their concomitant involvement in PAH solubilization and uptake. The transcriptional and translational regulators (secondary messenger cyclic-di-GMP, quorum sensing molecules, small ribosomal RNAs, two-component signaling molecules) control the synthesis of these ‘bioavailability enhancers’ towards PAH utilization and have been elucidated explicitly in the current review.
provides habitats to microorganisms. Changes in soil properties, productivity, and, inevitably co... more provides habitats to microorganisms. Changes in soil properties, productivity, and, inevitably contamination/ stress are the result of urbanisation, industrialization, and long-term use of synthetic fertiliser. Therefore, in the recent scenario, reclamation of contaminated/stressed soils has become a potential challenge. Several customized, such as, physical, chemical, and biological technologies have been deployed so far to restore contaminated land. Among them, microbial-assisted phytoremediation is considered as an economical and greener approach. In recent decades, soil microbes have successfully been used to improve plants’ ability to tolerate biotic and abiotic stress and strengthen their phytoremediation capacity. Therefore, in this context, the current review work critically explored the microbial assisted phytoremediation mechanisms to restore different types of stressed soil. The role of plant growth-promoting rhizobacteria (PGPR) and their potential mechanisms that foster plants’ growth and also enhance phytoremediation capacity are focussed. Finally, this review has emphasized on the application of advanced tools and techniques to effectively characterize potent soil microbial communities and their significance in boosting the phytoremediation process of stressed soils along with prospects for future research.
The green synthesis of nanoparticles (NPs) is the safest, ecofriendly, cost-effective, and non-ha... more The green synthesis of nanoparticles (NPs) is the safest, ecofriendly, cost-effective, and non-hazardous approach of nanotechnology. In the current study, we described the green synthesis of silver nanoparticles (AgNPs) using Cuphea carthagenensis aqueous leaf extract as a reducing, capping, and stabilizing agent. The study aims at the synthesis, characterization, optimization, and determination of the antibacterial activity of Cc-AgNPs against clinically important human pathogens. Coating of cotton fabrics with Cc-AgNPs and their efficacy against skin infection causing organisms was also evaluated. Furthermore, antioxidant activity, growth assay and time kill assay of Cc-AgNPs were also performed in the study. The biosynthesized Cc-AgNPs were characterized by UV-visible spectrometry, energy-dispersive X-ray spectroscopy (EDX), X-ray diffraction (XRD), transmission electron microscopy (TEM), and Fourier transform infrared spectroscopy (FTIR). The spectroscopic and microscopic analysis demonstrated biosynthesis of face-centered cubic (fcc) crystalline spherical Cc-AgNPs with an average particle size of 10.65 ± 0.1 nm. Optimized peak synthesis of Cc-AgNPs was reported at pH7, 55 °C, 4 mM silver nitrate, and 5:45 (plant extract: silver nitrate). Cc-AgNPs exhibited potent antioxidant effect and antibacterial activity against both Gram-positive and Gram-negative bacteria. The lowest MIC (15 μg/ml) and MBC (25 μg/ml) values were reported against S. typhimurium. The Cc-AgNPs coated fabrics demonstrated potent antibacterial activity against tested strains. This application could be helpful in wound healing management. Furthermore, the hemolytic analysis demonstrated that Cc-AgNPs exhibit non-toxic nature against Red Blood Cells (RBCs) at the tested concentrations. In conclusion, the investigation demonstrated a fast, stable, and eco-friendly approach to the biosynthesis of Cc-AgNPs along with their antibacterial and antioxidant properties.
Optimization and Applicability of Bioprocesses, 2017
Biofilms are resilient and complex microbial communities or populations encased in a self-produci... more Biofilms are resilient and complex microbial communities or populations encased in a self-producing extracellular matrix existing in nature, which account for their robustness against a wide variety of stresses. In nature, multispecies biofilms have been found to occur frequently, whereas monospecies biofilms have been rare and found only when developed. By understanding the sociobiology of biofilm bacteria and harnessing the knowledge based on known biochemical and physical parameters, the underlying complexity of biofilm microenvironment could be better predicted by state-of-the-art advanced modeling approaches. In the present review, in-depth advanced modeling approaches based on the action of substrates on developmental biofilm physiology have been discussed. Equations for forces and adherence, quorum sensing, fluid flow dynamics, the social arrangement of community members in their favorable places, stratification, and pattern formation inside the biofilm have been elaborated. Equations to predict biofilm dispersal stages have been also discussed. Different models which uncover microbial biofilm life cycle stages to predict their complexity and recommended future variables like “omics” for magnification have been reported. This chapter will help to provide additional platform related to the genetic complex networking of biofilm bacteria for conceptual underpinnings of biofilm microenvironment.
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Papers by Asifa Qureshi
Hydrophobic organic compounds, either natural or introduced through anthropogenic activities, pose a serious threat to all spheres of life, including humankind. These hydrophobic compounds are recalcitrant and difficult to degrade by the
microbial system; however, microbes have also evolved their metabolic and degradative potential. Pseudomonas species have been reported to have a multipotential role in the biodegradation of aromatic hydrocarbons through aromatic ringhydroxylating dioxygenases (ARHDs). The structural complexity of different hydrophobic substrates and their chemically inert nature demands the explicit role of evolutionary conserved multicomponent enzyme ARHDs. These enzymes
catalyze ring activation and subsequent oxidation by adding two molecular oxygen atoms onto the vicinal carbon of the aromatic nucleus. This critical metabolic step in the aerobic mode of degradation of polycyclic aromatic hydrocarbons (PAHs) catalyzed by ARHDs can also be explored through protein molecular docking studies. Protein data analysis enables an understanding of molecular processes and monitoring complex biodegradation reactions. This review summarizes the molecular characterization of five ARHDs from Pseudomonas species already reported for PAH degradation. Homology modeling for the amino acid sequences encoding the catalytic α-subunit of ARHDs and their docking analyses with PAHs suggested that the enzyme active sites show flexibility around the catalytic pocket for binding of low molecular
weight (LMW) and high molecular weight (HMW) PAH substrates (naphthalene, phenanthrene, pyrene, benzo[α]pyrene). The alpha subunit harbours variable catalytic pockets and broader channels, allowing relaxed enzyme specificity toward PAHs. ARHD’s ability to accommodate different LMW and HMW PAHs demonstrates its ‘plasticity’, meeting the catabolic demand of the PAH degraders
Hydrophobic organic compounds, either natural or introduced through anthropogenic activities, pose a serious threat to all spheres of life, including humankind. These hydrophobic compounds are recalcitrant and difficult to degrade by the
microbial system; however, microbes have also evolved their metabolic and degradative potential. Pseudomonas species have been reported to have a multipotential role in the biodegradation of aromatic hydrocarbons through aromatic ringhydroxylating dioxygenases (ARHDs). The structural complexity of different hydrophobic substrates and their chemically inert nature demands the explicit role of evolutionary conserved multicomponent enzyme ARHDs. These enzymes
catalyze ring activation and subsequent oxidation by adding two molecular oxygen atoms onto the vicinal carbon of the aromatic nucleus. This critical metabolic step in the aerobic mode of degradation of polycyclic aromatic hydrocarbons (PAHs) catalyzed by ARHDs can also be explored through protein molecular docking studies. Protein data analysis enables an understanding of molecular processes and monitoring complex biodegradation reactions. This review summarizes the molecular characterization of five ARHDs from Pseudomonas species already reported for PAH degradation. Homology modeling for the amino acid sequences encoding the catalytic α-subunit of ARHDs and their docking analyses with PAHs suggested that the enzyme active sites show flexibility around the catalytic pocket for binding of low molecular
weight (LMW) and high molecular weight (HMW) PAH substrates (naphthalene, phenanthrene, pyrene, benzo[α]pyrene). The alpha subunit harbours variable catalytic pockets and broader channels, allowing relaxed enzyme specificity toward PAHs. ARHD’s ability to accommodate different LMW and HMW PAHs demonstrates its ‘plasticity’, meeting the catabolic demand of the PAH degraders