Identifying and engineering a critical amino acid residue to enhance the catalytic efficiency of Pseudomonas sp. methyl parathion hydrolase

A Dual-Focus Workflow for Simultaneously Engineering High Activity and Thermal Stability in Methyl Parathion Hydrolase

Industrial fermentation applications typically require enzymes that exhibit high stability and activity at high temperatures. However, efforts to simultaneously improve these properties are usually limited by a trade-off between stability and activity. This report describes a computational strategy to enhance both activity and thermal stability of the mesophilic organophosphate-degrading enzyme, methyl parathion hydrolase (MPH). To predict hotspot mutation sites, we assembled a library of features associated with the target properties for each residue and then prioritized candidate sites by hierarchical clustering. Subsequent in silico screening with multiple algorithms to simulate selective pressures yielded a subset of 23 candidate mutations. Iterative parallel screening of mutations that improved thermal stability and activity yielded, MPHase-m5b, which exhibited 13.3 °C higher Tm and 4.2 times higher catalytic activity than wild-type (WT) MPH over a wide temperature range. Systematic analysis of crystal structures, molecular dynamics (MD) simulations, and quantum mechanics/molecular mechanics (QM/MM) calculations revealed a wider entrance to the active site that increased substrate access with an extensive network of interactions outside the active site that reinforced αβ/βα sandwich architecture to improve thermal stability. This study thus provides an advanced, rational design framework to improve efficiency in engineering highly active, thermostable biocatalysts for industrial applications.

Elucidating the Enzymatic Mechanism of Dihydrocoumarin Degradation: Insight into the Functional Evolution of Methyl-Parathion Hydrolase from QM/MM and MM MD Simulations

Methyl-parathion hydrolase (MPH), which evolved from dihydrocoumarin hydrolase, offers one of the most efficient enzymes for the hydrolysis of methyl-parathion. Interestingly, the substrate preference of MPH shifts from the methyl-parathion to the lactone dihydrocoumarin (DHC) after its mutation of five specific residues (R72L, L273F, L258H, T271I, and S193Δ, m5-MPH). Here, extensive QM/MM calculations and MM MD simulations have been used to delve into the structure-function relationship of MPH enzymes and plausible mechanisms for the chemical and nonchemical steps, including the transportation and binding of the substrate DHC to the active site, the hydrolysis reaction, and the product release. The results reveal that the five mutations remodel the active pocket and reposition DHC within the active site, leading to stronger enzyme-substrate interactions. The MM/GBSA-estimated binding free energies are about -20.7 kcal/mol for m5-MPH and -17.1 kcal/mol for wild-type MPH. Furthermore, this conformational adjustment of the protein may facilitate the chemical step of DHC hydrolysis and the product release, although there is a certain influence on the substrate transport. The hydrolytic reaction begins with the nucleophilic attack of the bridging OH- with the energy barriers of 22.0 and 18.0 kcal/mol for the wild-type and m5-MPH enzymes, respectively, which is rate-determining for the entire process. Unraveling these mechanistic intricacies may help in the understanding of the natural evolution of enzymes for diverse substrates and establish the enzyme structure-function relationship.

Identification and characterization of a promiscuous metallohydrolase in metallo-β-lactamase superfamily from a locally isolated organophosphate-degrading Bacillus sp. strain S3wahi

In this present study, characteristics and structure-function relationship of an organophosphate-degrading enzyme from Bacillus sp. S3wahi were described. S3wahi metallohydrolase, designated as S3wahi-MH (probable metallohydrolase YqjP), featured the conserved αβ/βα metallo-β-lactamase-fold (MBL-fold) domain and a zinc bimetal at its catalytic site. The metal binding site of S3wahi-MH also preserves the H-X-H-X-D-H motif, consisting of specific amino acids at Zn1 (Asp69, His70, Asp182, and His230) and Zn2 (His65, His67, and His137). The multifunctionality of S3wahi-MH was demonstrated through a steady-state kinetic study, revealing its highest binding affinity (KM) and catalytic efficiency (kcat/KM) for OP compound, paraoxon, with values of 8.09 × 10-6 M and 4.94 × 105 M-1 s-1, respectively. Using OP compound, paraoxon, as S3wahi-MH native substrate, S3wahi-MH exhibited remarkable stability over a broad temperature range, 20 °C - 60 °C and a broad pH tolerance, pH 6-10. Corresponded to S3wahi-MH thermal stability characterization, the estimated melting temperature (Tm) was found to be 72.12 °C. S3wahi-MH was also characterized with optimum catalytic activity at 30 °C and pH 8. Additionally, the activity of purified S3wahi-MH was greatly enhanced in the presence of 1 mM and 5 mM of manganese (Mn2+), showing relative activities of 1323.68 % and 2073.68 %, respectively. The activity of S3wahi-MH was also enhanced in the presence of DMSO and DMF, showing relative activities of 270.37 % and 307.41 %, respectively. The purified S3wahi-MH retained >60 % residual activity after exposure to non-ionic Tween series surfactants. Nevertheless, the catalytic activity of S3wahi-MH was severely impacted by the treatment of SDS, even at low concentrations. Considering its enzymatic properties and promiscuity, S3wahi-MH emerges as a promising candidate as a bioremediation tool in wide industrial applications, including agriculture industry.

Effective remediation and decontamination of organophosphorus compounds using enzymes: From rational design to potential applications

Organophosphorus compounds (OPs) have been widely used in agriculture for decades because of their high insecticidal efficiency, which maintains and increases crop yields worldwide. More importantly, OPs, as typical chemical warfare agents, are a serious concern and significant danger for military and civilian personnel. The widespread use of OPs, superfluous and unreasonable use, has caused great harm to the environment and food chain. Developing efficient and environmentally friendly solutions for the decontamination of OPs is a long-term challenge. Microbial enzymes show potential application as natural and green biocatalysts. Thus, utilizing OP-degrading enzymes for environmental decontamination presents significant advantages, as these enzymes can rapidly hydrolyze OPs; are environmentally friendly, nonflammable, and noncorrosive; and can be discarded safely and easily. Here, the properties, structure and catalytic mechanism of various typical OP-degrading enzymes are reviewed. The methods and effects utilized to improve the expression level, catalytic performance and stability of OP-degrading enzymes were systematically summarized. In addition, the immobilization of OP-degrading enzymes was explicated emphatically, and the latest progress of cascade reactions based on immobilized enzymes was discussed. Finally, the latest applications of OP-degrading enzymes were summarized, including biosensors, nanozyme mimics and medical detoxification. This review provides guidance for the future development of OP-degrading enzymes and promotes their application in the field of environmental bioremediation and medicine.

Improving Catalytic Activity and Thermal Stability of Methyl-Parathion Hydrolase for Degrading the Pesticide of Methyl-Parathion

Pesticides are indispensable in today’s agriculture. Methyl-parathion hydrolase (MPH, E.C.3.1.8.1) could hydrolyze organophosphorus pesticides, including methyl-parathion. MPH could rehabilitate soil and water resources contaminated by organophosphorus pesticides. However, natural MPHs generally exhibited a low tolerance to high temperatures and low catalytic efficiency. In this study, we improved the catalytic efficiency toward methyl-parathion and the thermal stability of the MPH from Pseudomonas sp. WBC-3 through saturation mutagenesis and fusion with self-assembling amphipathic peptides (SAP). The experimental characterization showed that compared to the wild-type enzyme, the kcat/Km of the mutant T271S yielded by saturation mutagenesis was increased by 224.3% compared to the wild-type MPH. T50 and Tm of SAP3-MPH with an SAP fused at the N-terminus were increased by 6.2°C and 6.0°C, respectively. Compared to the wild-type enzyme, T271S fused with SAP3 at the N-terminus (SAP3-T271S) exhibited a 2.1-fold increase in kcat/Km without significantly affecting the thermal stability. The simultaneous improvement of the catalytic efficiency and thermal stability of MPH would be beneficial for its application in the degradation and detection of organophosphorus pesticides. Furthermore, our study provides a potential combination strategy for the design of the other enzyme preparations of pollutant degradation.

A novel organophosphate hydrolase from Arthrobacter sp. HM01: Characterization and applications

Bioremediation systems coupled to efficient microbial enzymes have emerged as an attractive approach for the in-situ removal of hazardous organophosphates (OPs) pesticides from the polluted environment. However, the role of engineered enzymes in OPs-degradation is rarely studied. In this study, the potential OPs-hydrolase (opdH) gene (Arthrobacter sp. HM01) was isolated, cloned, expressed, and purified. The recombinant organophosphate hydrolase (ropdH) was ∼29 kDa; which catalyzed a broad-range of OPs-pesticides in organic-solvent (∼99 % in 30 min), and was found to increase the catalytic efficiency by 10-folds over the native enzyme (k_cat/K_m: 10⁷ M^-1s^-1). The degraded metabolites were analyzed using HPLC/GCMS. Through site-directed mutagenesis, it was confirmed that, conserved metal-bridged residue (Lys-127), plays a crucial role in OPs-degradation, which shows ∼18-folds decline in OPs-degradation. Furthermore, the catalytic activity and its stability has been enhanced by >2.0-fold through biochemical optimization. Thus, the study suggests that ropdH has all the required properties for OPs bioremediation.

Degradation insight of organophosphate pesticide chlorpyrifos through novel intermediate 2,6-dihydroxypyridine by Arthrobacter sp. HM01

Organophosphates (OPs) are hazardous pesticides, but an indispensable part of modern agriculture; collaterally contaminating agricultural soil and surrounding water. They have raised serious food safety and environmental toxicity that adversely affect the terrestrial and aquatic ecosystems and therefore, it become essential to develop a rapid bioremediation technique for restoring the pristine environment. A newly OPs degrading Arthrobacter sp. HM01 was isolated from pesticide-contaminated soil and identified by a ribotyping (16S rRNA) method. Genus Arthrobacter has not been previously reported in chlorpyrifos (CP) degradation, which shows 99% CP (100 mg L-1) degradation within 10 h in mMSM medium and also shows tolerance to a high concentration (1000 mg L-1) of CP. HM01 utilized a broad range of OPs pesticides and other aromatic pollutants including intermediates of CP degradation as sole carbon sources. The maximum CP degradation was obtained at pH 7 and 32 °C. During the degradation, a newly identified intermediate 2,6-dihydroxypyridine was detected through TLC/HPLC/LCMS analysis and a putative pathway was proposed for its degradation. The study also revealed that the organophosphate hydrolase (opdH) gene was responsible for CP degradation, and the opdH-enzyme was located intracellularly. The opdH enzyme was characterized from cell free extract for its optimum pH and temperature requirement, which was 7.0 and 50 °C, respectively. Thus, the results revealed the true potential of HM01 for OPs-bioremediation. Moreover, the strain HM01 showed the fastest rate of CP degradation, among the reported Arthrobacter sp.

Overview of a bioremediation tool: organophosphorus hydrolase and its significant application in the food, environmental, and therapy fields

In the past decades, the organophosphorus compounds had been widely used in the environment and food industries as pesticides. Owing to the life-threatening and long-lasting problems of organophosphorus insecticide (OPs), an effective detection and removal of OPs have garnered growing attention both in the scientific and practical fields in recent years. Bacterial organophosphorus hydrolases (OPHs) have been extensively studied due to their high specific activity against OPs. OPH could efficiently hydrolyze a broad range of substrates both including the OP pesticides and some nerve agents, suggesting a great potential for the remediation of OPs. In this review, the microbial identification, molecular modification, and practical application of OPHs were comprehensively discussed.Key points• Microbial OPH is a significant bioremediation tool against OPs.• Identification and molecular modification of OPH was discussed in detail.• The applications of OPH in food, environmental, and therapy fields are presented.

In-depth biochemical identification of a novel methyl parathion hydrolase from Azohydromonas australica and its high effectiveness in the degradation of various organophosphorus pesticides

Organophosphorus pesticides are highly toxic phosphate compounds with the general structure of O = P(OR)₃ and threaten human health seriously. Methyl parathion hydrolase from microbial is an important enzyme to degrade organophosphorus pesticides (OPs) into less toxic or nontoxic compounds like. p-nitrophenol and diethyl phosphate. Here, a gene encoding methyl parathion hydrolase from Azohydromonas australica was firstly cloned and expressed in Escherichia coli. The recombinant hydrolase showed its optimal pH and temperature at pH 9.5 and 50 °C. Leveraging 1 mM Mn²⁺, the enzyme activity was significantly enhanced by 29.3-fold, and the thermostability at 40 and 50 °C was also improved. The recombinant MPH showed the specific activity of 4.94 and 16.0 U/mg towards methyl parathion and paraoxon, respectively. Moreover, A. australica MPH could effectively degrade various of OPs pesticides including methyl parathion, paraoxon, dichlorvos and chlorpyrifos in a few minutes, suggesting a great potential in the bioremediation of OPs pesticides.

Mutagenesis for Improvement of Activity and Stability of Prolyl Aminopeptidase from Aspergillus oryzae

In this study, the prokaryotic expression system of Escherichia coli was used to modify prolyl aminopeptidase derived from Aspergillus oryzae JN-412 (AoPAP) via random mutagenesis and site-directed saturation mutagenesis. A random mutant library with a capacity of approximately 3000 mutants was compiled using error-prone polymerase chain reaction, and nonconservative amino acids within 3 Å of the substrate L-proline-p-nitroaniline were selected as site-directed saturation mutagenesis sites via homologous simulation and molecular docking of AoPAP. Variants featuring high catalytic efficiency were screened by a high-throughput screening method. The specific activities of the variants of 3D9, C185V, and Y393W were 127 U mg^-1, 156 U mg^-1, and 120 U mg^-1, respectively, which were 27%, 56%, and 20% higher than those of the wild type, with a value of 100 U mg^-1. The half-life of thermostability of the mutant 3D9 was 4.5 h longer than that of the wild type at 50 °C. The mutant C185V improved thermostability and had a half-life 2 h longer than that of the wild type at a pH of 6.5. Prolyl aminopeptidase had improved stability within the acidic range and thermostability after modification, making it more suitable for a synergistic combination with various acidic and neutral endoproteases.

Rapid Biodegradation of the Organophosphorus Insecticide Chlorpyrifos by Cupriavidus nantongensis X1T

Chlorpyrifos was one of the most widely used organophosphorus insecticides and the neurotoxicity and genotoxicity of chlorpyrifos to mammals, aquatic organisms and other non-target organisms have caused much public concern. Cupriavidus nantongensis X1^T, a type of strain of the genus Cupriavidus, is capable of efficiently degrading 200 mg/L of chlorpyrifos within 48 h. This is ~100 fold faster than Enterobacter B-14, a well-studied chlorpyrifos-degrading bacterial strain. Strain X1^T can tolerate high concentrations (500 mg/L) of chlorpyrifos over a wide range of temperatures (30–42 °C) and pH values (5–9). RT-qPCR analysis showed that the organophosphorus hydrolase (OpdB) in strain X1^T was an inducible enzyme, and the crude enzyme isolated in vitro could still maintain 75% degradation activity. Strain X1^T can simultaneously degrade chlorpyrifos and its main hydrolysate 3,5,6-trichloro-2-pyridinol. TCP could be further metabolized through stepwise oxidative dechlorination and further opening of the benzene ring to be completely degraded by the tricarboxylic acid cycle. The results provide a potential means for the remediation of chlorpyrifos- contaminated soil and water.

Asp305Gly mutation improved the activity and stability of the styrene monooxygenase for efficient epoxide production in Pseudomonas putida KT2440

Background

Styrene monooxygenase (SMO) catalyzes the first step of aromatic alkene degradation yielding the corresponding epoxides. Because of its broad spectrum of substrates, the enzyme harbors a great potential for an application in medicine and chemical industries.

Results

In this study, we achieved higher enzymatic activity and better stability towards styrene by enlarging the ligand entrance tunnel and improving the hydrophobicity through error-prone PCR and site-saturation mutagenesis. It was found that Asp305 (D305) hindered the entrance of the FAD cofactor according to the model analysis. Therefore, substitution with amino acids possessing shorter side chains, like glycine, opened the entrance tunnel and resulted in up to 2.7 times higher activity compared to the wild-type enzyme. The half-lives of thermal inactivation for the variant D305G at 60 °C was 28.9 h compared to only 3.2 h of the wild type SMO. Moreover, overexpression of SMO in Pseudomonas putida KT2440 with NADH regeneration was carried out in order to improve biotransformation efficiency for epoxide production. A hexadecane/buffer (v/v) biphasic system was applied in order to minimize the inactivation effect of high substrate concentrations on the SMO enzyme. Finally, SMO activities of 190 U/g CDW were measured and a total amount of 20.5 mM (S)-styrene oxide were obtained after 8 h.

Conclusions

This study offers an alternative strategy for improved SMO expression and provides an efficient biocatalytic system for epoxide production via engineering the entrance tunnel of the enzyme’s active site.

Electronic supplementary material

The online version of this article (10.1186/s12934-019-1065-5) contains supplementary material, which is available to authorized users.