Experimental and computational approaches to characterize a novel amidase that initiates the biodegradation of the herbicide propanil in Bosea sp. P5

Dual stimuli-responsive prodrug co-delivery nanosystem of salicylic acid and bioavailable silicon for long-term immunity in plant

Plant-induced resistance plays a crucial role in the plant defense system by activating intrinsic immune mechanisms. In this study, a novel amidase- and redox-responsive codelivery nanosystem was developed by covalently linking salicylic acid (SA) to functionalized disulfide-doped mesoporous silica nanoparticles (MSNs-ss-NH2) for the efficient delivery of SA and bioavailable silicon concurrently. Physicochemical characterization confirmed the successful preparation of MSNs-ss-SA, demonstrating its structural integrity and glutathione and amidase responsive degradation mechanism. With a particle size of approximately 90 nm, MSNs-ss-SA could penetrate the stomata of rice leaves, facilitating the efficient intracellular transport of SA and bioavailable silicon. Biological activity assays revealed that MSNs-ss-SA exhibited superior efficacy in inducing resistance to rice sheath blight compared to conventional SA, which was primarily due to its ability to enhance physical barrier formation, strengthen antioxidant defense systems, upregulate the expression of key defense-related genes, and increase chitinase synthesis, collectively triggering both systemic acquired resistance and induced systemic resistance. Most importantly, biological safety assessments confirmed its excellent compatibility with rice plants, aquatic organisms, soil ecosystems, and human cell models. Therefore, the prodrug system of SA and bioavailable silicon shows a significant potential for sustainable agricultural plant disease management.

A new strategy for removing insecticide etoxazole from soil using a combination of a novel Paracoccus versutus Y4 and a fungal mycelium carrier

Etoxazole is a widely used insecticide that poses a serious threat to both ecosystems and human health. In present study, a novel strain Paracoccus versutus Y4 was isolated and identified. More than 98 % of the etoxazole (10 mg/L) was degraded as the sole carbon source within 8 d by strain Y4 in liquid culture. HPLCMS/MS analysis revealed three possible intermediates, and a novel metabolic pathway of etoxazole including oxidation, dehydrogenation, and hydrolysis reactions was proposed. The Toxicity Estimation Software Tool suggests that the biodegradation intermediates were less harmful than etoxazole. Whole-genome sequencing revealed that the genome size of P. versutus Y4 was 5320,902 bp containing 5187 coding sequences. Among them, the gene coding monooxygenase, dehydrogenase and hydrolase may be responsible for etoxazole biodegradation. The results of molecular docking analysis suggested that the monooxygenase, dehydrogenase, and hydrolase from strain Y4 may facilitate catalytic degradation through efficient substrate binding. Compared with diatomite carrier, fungal mycelium carrier can promote the growth of strain Y4. In the soil degradation experiments, the fungal mycelium carrier promoted etoxazole degradation by strain Y4 in both fresh and sterilized soil. Treatment with Y4 +fungal mycelium significantly reduced the half-life of etoxazole in fresh soil from 24.2 to 6.3 d. Our study is the first to isolate etoxazole-degrading bacteria and provides a new strategy for the bioremediation of pesticide pollution by combining degrading microbes and fungal mycelium carriers.

Machine Learning Reveals Signatures of Promiscuous Microbial Amidases for Micropollutant Biotransformations

Organic micropollutants, including pharmaceuticals, personal care products, pesticides, and food additives, are widespread in the environment, causing potentially toxic effects. Human waste is a direct source of micropollutants, with the majority of pharmaceuticals being excreted through urine. Urine contains its own microbiota with the potential to catalyze micropollutant biotransformations. Amidase signature (AS) enzymes are known for their promiscuous activity in micropollutant biotransformations, but the potential for AS enzymes from the urinary microbiota to transform micropollutants is not known. Moreover, the characterization of AS enzymes to identify key chemical and enzymatic features associated with biotransformation profiles is critical for developing benign-by-design chemicals and micropollutant removal strategies. Here, to uncover the signatures of AS enzyme-substrate specificity, we tested 17 structurally diverse compounds against a targeted enzyme library consisting of 40 AS enzyme homologues from diverse urine microbial isolates. The most promiscuous enzymes were active on nine different substrates, while 16 enzymes had activity on at least one substrate and exhibited diverse substrate specificities. Using an interpretable gradient boosting machine learning model, we identified chemical and amino acid features associated with AS enzyme biotransformations. Key chemical features from our substrates included the molecular weight of the amide carbonyl substituent and the number of formal charges in the molecule. Four of the identified amino acid features were located in close proximity to the substrate tunnel entrance. Overall, this work highlights the understudied potential of urine-derived microbial AS enzymes for micropollutant biotransformation and offers insights into substrate and protein features associated with micropollutant biotransformations for future environmental applications.

Unveiling the analgesic and antipyretic drug acetaminophen catabolic mechanism in Pseudomonas taiwanensis AP-1

Acetaminophen (APAP), an analgesic and antipyretic drug, is commonly detected in wastewater treatment plant (WWTP) effluents, surface water, and soil, indicating its status as an emerging environmental contaminant. In this study, we isolated a bacterium, Pseudomonas taiwanensis AP-1, capable of completely mineralizing APAP and utilizing it as the sole carbon source for growth. A newly identified metabolite, γ-glutamyl-4-aminophenol (γ-G4AP), was reported for the first time in the degradation of APAP by strain AP-1. Two amidases (ApaH1 and ApaH2), responsible for the conversion of APAP to 4-aminophenol (4-AP), were identified through a combination of genomic comparison, heterologous expression, and gene knockout. Notably, ApaH1 played a pivotal role in the degradation of APAP by strain AP-1. The catalytic triad of ApaH1 (K82-S161-S185) and ApaH2 (K85-S160-S184) were identified as by molecular docking and site-directed mutagenesis. Additionally, a gene cluster apd for the metabolism of 4-AP was also successfully identified in strain AP-1, consisting of the aniline dioxygenase gene cluster apdBCD1D2EF and the BT catabolic gene apdGH. Interestingly, the 4-AP metabolic gene cluster apd was highly conserved among other Pseudomonas strains capable of APAP degradation. Our results provide new insights into the mechanism of APAP biodegradation and strain AP-1 may be a promising bacterium for the bioremediation of APAP pollutions.

Microbial degradation mechanisms of the neonicotinoids acetamiprid and flonicamid and the associated toxicity assessments

Extensive use of the neonicotinoid insecticides acetamiprid (ACE) and flonicamid (FLO) in agriculture poses severe environmental and ecological risks. Microbial remediation is considered a feasible approach to address these issues. Many ACE-and FLO-degrading microorganisms have been isolated and characterized, but few reviews have concentrated on the underlying degradation mechanisms. In this review, we describe the microbial degradation pathways of ACE and FLO and assess the toxicity of ACE, FLO and their metabolites. Especially, we focus on the enzymes involved in degradation of ACE and FLO, including cytochrome P450s, nitrile hydratases, amidases, and nitrilases. Those studies reviewed here further our understanding of the enzymatic mechanisms of microbial degradation of ACE and FLO, and aid in the application of microbes to remediate environmental ACE and FLO contamination.

Stenotrophomonas pavanii MY01 induces phosphate precipitation of Cu(II) and Zn(II) by degrading glyphosate: performance, pathway and possible genes involved

Microbial bioremediation is an advanced technique for removing herbicides and heavy metals from agricultural soil. In this study, the strain Stenotrophomonas pavanii MY01 was used for its ability to degrade glyphosate, a phosphorus-containing organic compound, producing PO4 3- as a byproduct. PO4 3- is known to form stable precipitates with heavy metals, indicating that strain MY01 could potentially remove heavy metals by degrading glyphosate. Therefore, the present experiment induced phosphate precipitation from Cu(II) (Hereinafter referred to as Cu2+) and Zn(II) (Hereinafter referred to as Zn2+) by degrading glyphosate with strain MY01. Meanwhile, the whole genome of strain MY01 was mined for its glyphosate degradation mechanism and its heavy metal removal mechanism. The results of the study showed that the strain degraded glyphosate best at 34°C, pH = 7.7, and an inoculum of 0.7%, reaching 72.98% within 3d. The highest removal of Cu2+ and Zn2+ in the test was 75.95 and 68.54%, respectively. A comparison of strain MY01's genome with glyphosate degradation genes showed that protein sequences GE000474 and GE002603 had strong similarity to glyphosate oxidoreductase and C-P lyase. This suggests that these sequences may be key to the strain's ability to degrade glyphosate. The GE001435 sequence appears to be related to the phosphate pathway, which could enable phosphate excretion into the environment, where it forms stable coordination complexes with heavy metals.

Mechanistic Insight into the Enantioselective Degradation of Esterase QeH to (R)/(S)-Quizalofop-Ethyl with Molecular Dynamics Simulation Using a Residue-Specific Force Field

The enantioselective mechanism of the esterase QeH against the two enantiomers of quizalofop-ethyl (QE) has been primitively studied using computational and experimental approaches. However, it is still unclear how the esterase QeH adjusts its conformation to adapt to substrate binding and promote enzyme-substrate interactions in the catalytic kinetics. The equilibrium processes of enzyme-substrate interactions and catalytic dynamics were reproduced by performing independent molecular dynamics (MD) runs on the QeH-(R)/(S)-QE complexes with a newly developed residue-specific force field (RSFF2C). Our results indicated that the benzene ring of the (R)-QE structure can simultaneously form anion-π and cation-π interactions with the side-chain group of Glu328 and Arg384 in the binding cavity of the QeH-(R)-QE complex, resulting in (R)-QE being closer to its catalytic triplet system (Ser78-Lys81-Tyr189) with the distances measured for the hydroxyl oxygen atom of the catalytic Ser78 of QeH and the carbonyl carbon atom of (R)-QE of 7.39 Å, compared to the 8.87 Å for (S)-QE, whereas the (S)-QE structure can only form an anion-π interaction with the side chain of Glu328 in the QeH-(S)-QE complex, being less close to its catalytic site. The computational alanine scanning mutation (CAS) calculations further demonstrated that the π-π stacking interaction between the indole ring of Trp351 and the benzene ring of (R)/(S)-QE contributed a lot to the binding stability of the enzyme-substrate (QeH-(R)/(S)-QE). These results facilitate the understanding of their catalytic processes and provide new theoretical guidance for the directional design of other key enzymes for the initial degradation of aryloxyphenoxypropionate (AOPP) herbicides with higher catalytic efficiencies.

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.

Characterization of a novel amidohydrolase with promiscuous esterase activity from a soil metagenomic library and its application in degradation of amide herbicides

Amide herbicides have been extensively used worldwide and have received substantial attention due to their adverse environmental effects. Here, a novel amidohydrolase gene was identified from a soil metagenomic library using diethyl terephthalate (DET) as a screening substrate. The recombinant enzyme, AmiH52, was heterologously expressed in Escherichia coli and later purified and characterized, with the highest activity occurring at 40 ℃ and pH 8.0. AmiH52 was demonstrated to have both esterase and amidohydrolase activities, which exhibited highly specific activity for p-nitrophenyl butyrate (2669 U/mg) and degrading activity against several amide herbicides. In particular, it displayed the strongest activity against propanil, with a high degradation rate of 84% at 8 h. A GC-MS analysis revealed that propanil was transformed into 3,4-dichloroaniline (3,4-DCA) during this degradation. The molecular interactions and binding stability were then analyzed by molecular docking and molecular dynamics simulation, which revealed that several key amino acid residues, including Tyr164, Trp66, Ala59, Val283, Arg58, His33, His191, and His226, are involved in the specific interactions with propanil. This study provides a function-driven screening method for amide herbicide hydrolase from the metagenomic libraries and a promising propanil-degrading enzyme (AmiH52) for potential applications in environmental remediation.

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.

Design and characterization of antithrombotic ClEKnsTy-Au nanoparticles as diagnostic and therapeutic reagents

Thrombosis can cause various cardiovascular diseases, which seriously endanger human life. Development of diagnostic and therapeutic reagents for thrombosis at an early stage would be helpful for the improvement of treatment and the reduction of mortality. In the present study, based on an antithrombotic peptide lEKnsTy (lowercase letters represent D-amino acid residues), a diagnostic and therapeutic reagent targeting collagen and the early stage of thrombosis was proposed, where cysteine was introduced into the amino terminus of lEKnsTy to prepare ClEKnsTy, followed by coupling with AuNPs to prepare nanoconjugate AuNP-Cl. The binding of AuNP-Cl on the collagen surface was then confirmed by the molecular dynamics simulations of the binding of ClEKnsTy on collagen, and the experimental results of the binding of AuNP-Cl on collagen. The inhibition of platelet adhesion on the collagen surface by AuNP-Cl was also confirmed. Moreover, the good imaging ability of AuNP-Cl was confirmed by dark-field microscopy. These results indicated that AuNP-Cl was a potential effective diagnostic and therapeutic reagent targeting collagen, which would be helpful for the research and development of multifunctional antithrombotic reagents.