A bifunctional enzyme belonging to cytochrome P450 family involved in the O-dealkylation and N-dealkoxymethylation toward chloroacetanilide herbicides in Rhodococcus sp. B2

Novel Bifunctional Amidase Catalyzing the Degradation of Propanil and Aryloxyphenoxypropionate Herbicides in Rhodococcus sp. C-1

Propanil residues can contaminate habitats where microbial degradation is predominant. In this study, an efficient propanil-degrading strain C-1 was isolated from paddy and identified as Rhodococcus sp. It can completely degrade 10 μg/L-150 mg/L propanil within 0.33-10 h via the hydrolysis of the amide bond, forming 3,4-dichloroaniline. A novel bifunctional amidase, PamC, was identified in strain C-1. PamC can catalyze the hydrolysis of the amide bond of propanil to produce 3,4-dichloroaniline as well as the hydrolysis of the ester bonds of aryloxyphenoxypropionate herbicides (APPHs, clodinafop-propargyl, cyhalofop-butyl, fenoxaprop-p-ethyl, fluazifop-p-butyl, haloxyfop-p-methyl, and quizalofop-p-ethyl) to form aryloxyphenoxypropionic acids. Molecular docking and site-directed mutagenesis confirmed that the catalytic triad Lys82-Ser157-Ser181 was the active center for PamC to hydrolyze propanil and cyhalofop-butyl. This study presents a novel bifunctional amidase with capabilities for both amide and ester bond hydrolysis and enhances our understanding of the molecular mechanisms underlying the degradation of propanil and APPHs.

Degradation of pretilachlor and fenclorim and effects of these compounds on bacterial communities under anaerobic condition

Pretilachlor and safener fenclorim are the main components of herbicides widely applied to control weeds. Although some pure cultures of bacteria and fungi which degraded these compounds under aerobic conditions were isolated, no isolated pretilachlor- and fenclorim-degrading bacterial strains under anaerobic condition had been available. In this study, the degradation of these compounds and the effects of them on bacterial community structures were investigated under anaerobic conditions. The dissipation rates of pretilachlor and fenclorim in slurries were in the order: soil from paddy field ≈ sediment from river > sediment from mangrove. Moreover, three pretilachlor-degrading bacterial strains (Pseudomonas sp. Pr1, Proteiniclasticum sp. Pr2 and Paracoccus denitrificans Pr3) and two fenclorim-degrading strains (Dechloromonas sp. Fe1 and Ralstonia pickettii Fe2) isolated from a slurry of paddy soil utilized the substrates as sole carbon and energy sources under anaerobic conditions. The degradation of pure pretilachlor and fenclorim at various concentrations by corresponding mixed pure cultures followed the Michaelis-Menten model, with the maximum degradation was 3.10 ± 0.31 µM/day for pretilachlor, and 2.08 ± 0.18 µM/day for fenclorim. During the degradation, 2-chloro-N-(2,6-diethylphenyl) acetamide and 2,6-dimethylaniline were produced in pretilachlor degradation, and benzene was a product of fenclorim degradation. The synergistic degradation of both substrates by all isolated bacteria reduced the metabolites concentrations accumulated in media. This study provides valuable information on effects of pretilachlor and fenclorim on bacterial communities in soil and sediments, and degradation of these substrates by isolated bacteria under anaerobic condition.

A novel pbd gene cluster responsible for pyrrole and pyridine ring cleavage in Rhodococcus ruber A5

Pyridine and pyrrole, which are regarded as recalcitrant chemicals, are released into the environment as a result of industrial manufacturing processes, posing serious hazards to both the environment and human health. However, the pyrrole degradation mechanism and the pyridine-degrading gene in Rhodococcus are unknown. Herein, a highly efficient pyridine and pyrrole degradation strain Rhodococcus ruber A5 was isolated. Strain A5 completely degraded 1000 mg/L pyridine in a mineral salt medium within 24 h. The pyridine degradation of strain A5 was optimized using the BoxBehnken design. The optimum degradation conditions were found to be pH 7.15, temperature 28.06 ℃, and inoculation amount 1290.94 mg/L. The pbd gene clusters involved in pyridine degradation were discovered via proteomic analysis. The initial ring cleavage of pyridine and pyrrole in strain A5 was carried out by the two-component flavin-dependent monooxygenase PbdA/PbdE. The degradation pathways of pyridine and pyrrole were proposed by the identification of metabolites and comparisons of homologous genes. Additionally, homologous pbd gene clusters were found to exist in different bacterial genomes. Our study revealed the ring cleavage mechanisms of pyrrole and pyridine, and strain A5 was identified as a promising resource for pyridine bioremediation.

Ultimate fate, transformation, and toxicological consequences of herbicide pretilachlor to biotic components and associated environment: An overview

Herbicides are applied for effective weed management in order to increase the crop yield. In recent decades, the overuse of these chemicals has posed adverse effects on different biotic components of the environment. Pretilachlor has been widely used during last few decades for weed management in paddy crop. Its excessive use may prove fatal for environment, various organisms, and nontarget plants. Thus, it is pertinent to know the extent to which herbicide residues remain in environment. The potential mobility and the release rate of herbicide in the soil are important factors governing ecotoxicological impact and degradation rate. Therefore, several techniques are being investigated for its effective removal from the contaminated sites. Furthermore, efforts have also been made to study the degradation of pretilachlor by various physicochemical processes, resulting into the formation of different types of metabolites. This review summarizes the available information on environmental fate, various degradation processes, microbial biotransformation, metabolites formed, ecotoxicological effects, techniques for detection in environmental samples, effect of safener, and various control release formulations for sustained release of pretilachlor in applied fields. The information so obtained will be very advantageous in deciding the future policies for safe and judicious use of the herbicide by maintaining health and environmental sustainability.

Mechanism of safener mefenpyr-diethyl biodegradation by a newly isolated Chryseobacterium sp. B6 from wastewater sludge and application in co-contaminated soil

Safener mefenpyr-diethyl (MFD) was applied to cereal crops along with herbicides to improve herbicide selectivity for crops and weeds. However, the degradation mechanism of MFD in the environment remains unclear. One MFD-degrading bacterium, Chryseobacterium sp. B6, was isolated from activated sludge. According to Box-Behnken's optimal design, the degradation efficiency of MFD can reach 92% under conditions of pH 7.5, 30 °C, and a MFD concentration of 184 mg L-1. The degradation half-life experiment showed that a high concentration of MFD (300 mg L-1) inhibited the degradation ability of strain B6. Additionally, strain B6 was resistant to Ba2+, Cr3+, Li+, Zn2+, and Cu2+. The MFD degradation products of strain B6 were detected by GC/MS and its degradation pathway was proposed. MFD was first hydrolyzed by a hydrolase to an intermediate (RS)-1-(2,4-dichlorophenyl)-5-methyl-2-pyrazoline-5-carboxylic acid ethyl ester-3-carboxylic acid, and then further degraded by a decarboxylase to form the intermediate (RS)-1-(2,4-dichlorophenyl)-5-methyl-2-pyrazoline-5-carboxylic acid ethyl ester, finally, it is completely degraded by strain B6. Furthermore, strain B6 could effectively remove MFD from MFD-contaminated soil, and the half-life of MFD was also significantly reduced in MFD and Cu2+ co-contaminated soil after inoculating strain B6. To our knowledge, strain B6 was the first strain reported to degrade safener MFD, and this study provides a valuable candidate to remediate the co-contaminated soil with MFD and Cu2+.

Biomineralization of pretilachlor by free and immobilized fungal strains isolated from paddy field

The excessive use of pretilachlor (a chloroacetamide herbicide) has raised concern throughout the world as it has been reported as highly toxic. The present study deals with isolating and screening pretilachlor degrading fungal strains. The strains Aspergillus ficuum (AJN2) and Aspergillus sp. (PDF1) isolated using enrichment technique were able to degrade 79% and 73% of pretilachlor respectively as analyzed using HPLC. Further, the immobilization technique was used in the study the pretilachlor degradation ability of the isolated strains. The immobilized spores of the strains AJN2 and PDF1 mineralized 84% and 95% of pretilachlor respectively. The degradation dynamics study revealed that the DT50 value of the herbicide was reduced to 2.4 d in aqueous medium due to the enhanced enzymatic activity. The enzymatic study showed high lignin peroxidase and manganese peroxidase activity by the strains AJN2 and PDF1 respectively. The study confirmed the efficient degradation of pretilachlor by Aspergillus ficuum (AJN2).

Efficient heterologous expression of cytochrome P450 enzymes in microorganisms for the biosynthesis of natural products

Natural products, a chemically and structurally diverse class of molecules, possess a wide spectrum of biological activities, have been used therapeutically for millennia, and have provided many lead compounds for the development of synthetic drugs. Cytochrome P450 enzymes (P450s, CYP) are widespread in nature and are involved in the biosynthesis of many natural products. P450s are heme-containing enzymes that use molecular oxygen and the hydride donor NAD(P)H (coupled via enzymic redox partners) to catalyze the insertion of oxygen into C-H bonds in a regio- and stereo-selective manner, effecting hydroxylation and several other reactions. With the rapid development of systems biology, numerous novel P450s have been identified for the biosynthesis of natural products, but there are still several challenges to the efficient heterologous expression of active P450s. This review covers recent developments in P450 research and development, including the properties and functions of P450s, discovery and mining of novel P450s, modification and screening of P450 mutants, improved heterologous expression of P450s in microbial hosts, efficient whole-cell transformation with P450s, and current applications of P450s for the biosynthesis of natural products. This resource provides a solid foundation for the application of highly active and stable P450s in microbial cell factories to biosynthesize natural products.

Revealing the driving synergistic degradation mechanism of Rhodococcus sp. B2 on the bioremediation of pretilachlor-contaminated soil

The pretilachlor has been widely used worldwide and has contaminated the environment for many years. The environmental fate of pretilachlor and its residues removal from the contaminated environment have attracted great concern. Reportedly, pretilachlor could partly be transformed to HECDEPA by Rhodococcus sp. B2. However, the effects of pretilachlor on soil bacterial communities and its complete metabolic pathway remain unknown. Herein, we investigated the mechanism of driving synergistic degradation of pretilachlor by strain B2 in the soil. The results revealed that pretilachlor showed a negative effect on bacterial communities and caused significant variations in the community structure. Strain B2 showed the ability to remediate the pretilachlor-contaminated soils and network analysis revealed that it may drive the enrichment of potential pretilachlor-degrading bacteria from the soil. The soil pretilachlor degradation may be facilitated by the members of the keystone families Comamonadaceae, Caulobacteraceae, Rhodospirillaceae, Chitinophagaceae, and Sphingomonadaceae. Meanwhile, Sphingomonas sp. M6, a member of the Sphingomonadaceae family, has been isolated from the strain B2 inoculation sample soil. The co-culture, comprising strain M6 and B2, could synergistic degrade pretilachlor within 30 h, which is the highest degradation rate. Strain M6 could completely degrade the HECDEPA via CDEPA and DEA. In the soil, a comparable pretilachlor degradation pathway may exist. This study suggested that strain B2 had the potential to drive the remediation of pretilachlor-contaminated soils.

Current state and future perspectives of cytochrome P450 enzymes for C–H and C=C oxygenation

Cytochrome P450 enzymes (CYPs) catalyze a series of C–H and C=C oxygenation reactions, including hydroxylation, epoxidation, and ketonization. They are attractive biocatalysts because of their ability to selectively introduce oxygen into inert molecules under mild conditions. This review provides a comprehensive overview of the C–H and C=C oxygenation reactions catalyzed by CYPs and the various strategies for achieving higher selectivity and enzymatic activity. Furthermore, we discuss the application of C–H and C=C oxygenation catalyzed by CYPs to obtain the desired chemicals or pharmaceutical intermediates in practical production. The rapid development of protein engineering for CYPs provides excellent biocatalysts for selective C–H and C=C oxygenation reactions, thereby promoting the development of environmentally friendly and sustainable production processes.