Biotransformation Mechanisms Research Articles

Transcriptome Profiling of Stenotrophomonas sp. Strain WZN-1 Reveals Mechanisms of 2,2',4,4'-Tetrabromodiphenyl Ether (BDE-47) Biotransformation.

The brominated flame retardant 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) is extensively used, stable, and difficult to degrade in the environment. The existence of BDE-47 could pose a certain risk to the environment and human health. However, the biotransformation mechanisms of BDE-47 by microorganisms remain unclear. In this study, aerobic degradation of BDE-47 by Stenotrophomonas sp. strain WZN-1 and transcriptome analysis were carried out. BDE-47 degradation by Stenotrophomonas sp. strain WZN-1 was mainly through the biological action of intracellular enzymes via the route of debromination and hydroxylation. The results of the transcriptome sequencing indicated the differentially expressed genes were related to transport, metabolism, and stress response. The key processes involved the microbial transmembrane transportation of BDE-47, energy anabolism, synthesis, and metabolism of functional enzymes, stress response, and other biological processes of gene regulation. In particular, bacterial chemotaxis played a potential role in biodegradation of BDE-47 by Stenotrophomonas sp. strain WZN-1. This study provides the first insights into the biotransformation of Stenotrophomonas sp. strain WZN-1 to BED-47 stress and shows potential for application in remediation of polluted environments.

Fate and Transformation of 6:2 Fluorotelomer Sulfonic Acid Affected by Plant, Nutrient, Bioaugmentation, and Soil Microbiome Interactions.

6:2 Fluorotelomer sulfonic acid (6:2 FTSA) is a dominant per- and poly-fluoroalkyl substance (PFAS) in aqueous film-forming foam (AFFF)-impacted soil. While its biotransformation mechanisms have been studied, the complex effects from plants, nutrients, and soil microbiome interactions on the fate and removal of 6:2 FTSA are poorly understood. This study systematically investigated the potential of phytoremediation for 6:2 FTSA byArabidopsis thalianacoupled with bioaugmentation ofRhodococcus jostiiRHA1 (designated as RHA1 hereafter) under different nutrient and microbiome conditions. Hyperaccumulation of 6:2 FTSA, defined as tissue/soil concentration > 10 and high translocation factor > 3, was observed in plants. However, biotransformation of 6:2 FTSA only occurred under sulfur-limited conditions. Spiking RHA1 not only enhanced the biotransformation of 6:2 FTSA in soil but also promoted plant growth. Soil microbiome analysis uncovered Rhodococcus as one of the dominant species in all RHA1-spiked soil. Different nutrients such as sulfur and carbon, bioaugmentation, and amendment of 6:2 FTSA caused significant changes in - microbial community structure. This study revealed the synergistic effects of phytoremediation and bioaugmentation on 6:2 FTSA removal. and highlighted that the fate of 6:2 FTSA was highly influced by the complex interactions of plants, nutrients, and soil microbiome.

Transformation mechanism of carbon tetrachloride and the associated micro-ecology in landfill cover, a typical functional layer zone

Landfill is one of the important sources of carbon tetrachloride (CT) pollution, and it is important to understand the degradation mechanism of CT in landfill cover for better control. In this study, a simulated landfill cover system was set up, and the biotransformation mechanism of CT and the associated micro-ecology were investigated. The results showed that three stable functional zones along the depth, i.e., aerobic zone (0-15 cm), anoxic zone (15-45 cm) and anaerobic zone (> 45 cm), were generated because of long-term biological oxidation in landfill cover. There were significant differences in redox condition and microbial community structure in each zone, which provided microbial resources and favorable conditions for CT degradation. The results of biodegradation indicated that dechlorination of CT produced chloroform (CF), dichloromethane (DCM) and Cl- in anaerobic and anoxic zones. The highest concentration of dechlorination products occurred at 30 cm, which were degraded rapidly in aerobic zone. In addition, CT degradation rate was 13.2-103.6 μg/(m2·d), which decreased with the increase of landfill gas flux. The analysis of diversity sequencing revealed that Mesorhizobium, Thiobacillus and Intrasporangium were potential CT-degraders in aerobic, anaerobic and anoxic zone, respectively. Moreover, six species of dechlorination bacteria and eighteen species of methanotrophs were also responsible for anaerobic transformation of CT and aerobic degradation of CF and DCM, respectively. Interestingly, anaerobic dechlorination and aerobic transformation occurred simultaneously in the anoxic zone in landfill cover. Furthermore, analysis of degradation mechanism suggested that generation of stable anaerobic-anoxic-aerobic zone by regulation was very important for the harmless removal of full halogenated hydrocarbon in vadose zone, and the increase of anoxic zone scale enhanced their removal. These results provide theoretical guidance for the removal of chlorinated pollutants in landfills.

The potential of biological agents in soil disinfection when contaminated with toxic chemicals

Pesticides have been widely used to control weeds, diseases and pests of cultivated plants all over the world, mainly since the mid-twentieth century. Pesticides are very widely used for pest control in many countries. The persistent nature of most synthetic pesticides causes serious environmental problems. Decontamination of these dangerous chemicals is very important. This review paper examines the potential of various biological agents in the disinfection of agricultural soils. The fields of agricultural crops are polluted by the periodic use of pesticides. Biodegradation is an eco-friendly, economical, highly effective approach compared to expensive and environmentally hazardous physical and chemical methods. Biodegradation is sensitive to the concentration levels of hydrogen peroxide and nitrogen, as well as to changes in the microbial community, temperature and acidity. Experimental work for optimal conditions on a laboratory scale can give very fruitful results about specific strains of bacteria and fungi. This study revealed the advantage of bioremediation over physico-chemical approaches. Further research should be conducted to understand the mechanisms of biotransformation.

Biotransformation of graphene oxide within lung fluids could intensify its synergistic biotoxicity effect with cadmium by inhibiting cellular efflux of cadmium

Graphene oxide (GO) has been widely studied and applied in numerous industrial fields and biomedical fields for its excellent physical and chemical properties. Along with the production and applications of GO persist increasing, the environmental health and safety risk (EHS) of GO has been widely studied. However, previous studies almost focused on the biotoxicity of pristine GO under a relatively high exposure dose, without considering its transformation process within environmental and biological mediums. Meanwhile, its secondary toxicity or synergistic effects have not been taken seriously. Here, two different kinds of artificial lung fluids were adopted to incubate pristine GO to mimic the biotransformation process of GO in the lung fluids. And, we explored that biotransformation within the artificial lung fluids could significantly change the physicochemical properties of GO and could enhance its biotoxicity. To reveal the synergistic effects of GO and toxic metal ions, we uncovered that GO could enhance the intracellular content of metal ions by inhibiting the efflux function of ATP binding cassette (ABC) transporters which are distributed on the cellular membrane, and artificial lung fluids incubation of GO could enhance this synergistic effect. Finally, toxic metal ions induced a series of toxic reactions through oxidative stress response and promoted cell death. Moreover, consistent with the results of in vitro experiments, the lungs of mice exposed to GOs combined with Cd exhibited significant inflammation and oxidative stress compared with Cd treatment alone, and it was more remarkable within the mice which were treated with bio-transformed GOs. In summary, this study explored the impact and mechanism of biotransformation of GO in the lung fluids on the synergistic and secondary effects between GO and metal ions.

Authenticity and traceability of goat milk: Molecular mechanism of β-carotene biotransformation and accessibility

The efficiently extraction and accurately quantify of β-carotene and its metabolites are crucial for authenticity and traceability in goat milk. Nevertheless, its reliability can be largely improved. In this study, meticulously designed native ESI-MS, fluorescence spectroscopy and molecular docking in combination with cold-induced acetonitrile aqueous two-phase separation system weaken the interaction between β-lactoglobulin and β-carotene metabolites and realized the efficiently extraction. Furthermore, established non-targeted quantitative metabolomics with optimal ion source and variable data-independent acquisition minimized the matrix effects and potential ion suppression. Validated atmospheric pressure chemical ionization-ultra high performance liquid chromatography-Orbitrap method showed that β-carotene as distinctive biomarker in cow milk, and retinol, retinaldehyde, retinoic acid and abscisic acid in goat milk. Collectively, the proposed method is a powerful tool to detect cow adulteration risks in goat milk samples and provides valuable information for availability on authenticity of goat milk.

Molecular targets for the development of new acaricides against Rhipicephalus microplus: a review.

The cattle tick Rhipicephalus microplus is an ectoparasite with high economic importance to bovine culture, mainly in tropical and subtropical regions. The resistance of the tick from the commercial acaricides has hindered its control, thus motivating the search for new strategies. The purpose of this study was to perform a critical review about the main molecular targets of R. microplus that are useful for the discovery of new acaricides. Bibliographic search was conducted in the databases PubMed, ScienceDirect and CAB Direct, using the following descriptors: ‘Rhipicephalus microplus’, ‘Boophilus microplus’, ‘molecular targets’ and ‘action’, published between 2010 and 2021. Out of the 212 publications identified, 17 articles were selected for study inclusion. This review described 14 molecular targets and among these 4 are targets from commercial acaricides. Most of them are enzymes to catalyse important reactions to tick survival, related to energetic metabolism, mechanisms of biotransformation and neurotransmission. The data will be helpful in the development of new more effective and selective acaricides.

Cytochromes P450: Role in Carcinogenesis and Relevance to Cancers

Cancer is a leading cause of mortality globally. Cytochrome P450 (CYP) enzymes play a pivotal role in the biotransformation of both endogenous and exogenous compounds. Various lines of evidence from epidemiological, animal, and clinical studies point to the instrumental role of CYPs in cancer initiation, metastasis, and prevention. Substantial research has found that CYPs are involved in activating different carcinogenic chemicals in the environment, such as polycyclic aromatic hydrocarbons and tobacco-related nitrosamines. Electrophilic intermediates produced from these chemicals can covalently bind to DNA, inducing mutation and cellular transformation that collectively result in cancer development. While bioactivation of procarcinogens and promutagens by CYPs has long been established, the role of CYP-derived endobiotics in carcinogenesis has only emerged in recent years. Eicosanoids derived from arachidonic acid via CYP oxidative pathways have been implicated in tumorigenesis, cancer progression and metastasis. The purpose of this review is to update the current state of knowledge about the molecular cancer mechanism involving CYPs with a focus on the biochemical and biotransformation mechanisms in the various CYP-mediated carcinogenesis and the role of CYP-derived reactive metabolites, from both external and endogenous sources, in cancer growth and tumor formation.

Biochemical response of Ficopomatus enigmaticus adults after exposure to organic and inorganic UV filters

With the increase of UV filters usage and consequent release into aquatic environments, the concerns about their potential ecological risks are also increasing. According to this, in the present study, adult polychaetes of the species Ficopomatus enigmaticus were chronically exposed to three concentrations (0.01, 0.1 and 0.5 mg/L) of organic and inorganic filters (Ethylhexyl methoxycinnamate (EHMC) and nanoparticulate Zinc oxide (nZnO), respectively) in order to analyse biochemical responses related to cellular damage, antioxidant defence, biotransformation mechanisms and, lastly, neurotoxicity. Despite major lipid peroxidation caused by EHMC was observed, both UV filters have produced the same response patterns. In details, a clear concentration-dependent activation of glutathione S-transferases and a significant decrease of acetylcholinesterase levels defined an important neurotoxic effect was observed for both contaminants. These results become important to expand the limited scientific literature on biochemical responses of marine and brackish water invertebrates to organic and inorganic UV filters.

Kinetic isotope effects of C and N indicate different transformation mechanisms between atzA- and trzN-harboring strains in dechlorination of atrazine.

Compound-specific stable isotope analysis provides an alternative method to insight into the biotransformation mechanisms of diffuse organic pollutants in the environment, e.g., the endocrine disruptor herbicide atrazine. Biotic hydrolysis process catalyzed by chlorohydrolase AtzA and TrzN plays an important role in the detoxification of atrazine, while the catalytic mechanism of AtzA is still speculative. To investigate the catalytic mechanism of AtzA and answer whether both enzymes catalyze hydrolytic dechlorination of atrazine by the same mechanism, in this study, apparent kinetic isotope effects (AKIE) for carbon and nitrogen were observed by three atzA-harboring bacterial isolates and their membrane-free extracts. The AKIEs obtained from atzA-harboring bacterial isolates (AKIEC = 1.021 ± 0.010, AKIEN = 0.992 ± 0.003) were statistically different from that of trzN-harboring strains (AKIEC = 1.040 ± 0.006, AKIEN = 0.983 ± 0.006), confirming the different activation mechanisms of atrazine preceding to nucleophilic aromatic substitution of Cl atom in actual enzymatic reaction catalyzed by AtzA and TrzN, despite the limitation of variable dual-element isotope plots. The lower degree of normal carbon and inverse nitrogen isotope fractionation observed from atzA-harboring strains, suggesting AtzA catalyzing hydrolytic dechlorination of atrazine by coordination of Cl and one aromatic N to the Fe2+ drawing electron density from carbon-chlorine bond that facilitating the nucleophilic attack, rather than in TrzN case that protonation of aromatic N increasing nucleophilic substitution of Cl atom. This study suggests considering the potential influences of phylogenetic diversity of bacterial isolates and evolution of enzymes on the applications of CSIA method in future study.

Microbial Biomass, Composition, and Functions Are Responsible for the Differential Removal of Trace Organic Chemicals in Biofiltration Systems: A Batch Study

Biofiltration processes help to remove trace organic chemicals (TOrCs) both in wastewater and drinking water treatment systems. However, the detailed TOrCs biotransformation mechanisms as well as the underlying drivers behind the variability of site specific transformation processes remain elusive. In this study, we used laboratory batch incubations to investigate the biotransformation of 51 TOrCs in eight bioactive filter materials of different origins treating a range of waters, from wastewater effluents to drinking water. Microscopy, 16S rRNA amplicon and whole metagenome sequencing for assessing associations between the biotransformation rate constants, microbial composition and genetic potential complemented chemical analysis. We observed strong differences in the mean global removal of TOrCs between the individual sand filters (−1.4–58%), which were mirrored in overall biomass, microbial community composition, and enzyme encoding genes. From the six investigated biomass markers, ATP turned out to be a major predictor of the mean global biotransformation rate, while compound specific biotransformations were correlated with the microbial community composition. High biomass ecosystems were indicated in our systems by a dominance of Nitrospirae, but individual TOrC biotransformation showed a correlation with rare taxa (<2%) such as Hydrogenophaga, or individual functions such as the enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase encoding genes. In general, this study provides new insights into so far rarely addressed variability of TOrCs biotransformation. We propose potential novel biological indicators for the removal performance of TOrCs in biofiltration systems, highlighting the role of living biomass in predicting and normalizing the global transformation, and the role of the microbial community for the individual transformation of TOrCs in engineered and natural systems.

Environmental Biotransformation Mechanisms by Flavin-Dependent Monooxygenase: A Computational Study

Environmental Biotransformation Mechanisms by Flavin-Dependent Monooxygenase: A Computational Study

Microbial Biotransformation Mechanisms of Pfpias in Soil Unveiled by Metagenomic Analysis

Microbial Biotransformation Mechanisms of Pfpias in Soil Unveiled by Metagenomic Analysis

Deciphering the Biotransformation Mechanism of Dialkylresorcinols by CYP4F11

Deciphering the Biotransformation Mechanism of Dialkylresorcinols by CYP4F11

Site of Metabolism (SOM) Predictions for Centella asiatica and Orthosiphon stamineus Marker Compounds with CYP3A4 Using a Molecular Docking Approach

The human liver enzyme CYP3A4 plays an important role in the biotransformation of xenobiotics from herbs to harmless and excretable metabolites. However, CYP3A4 catalytic activity may also produce more toxic metabolites. Predicting sites of metabolism (SOMs) in the xenobiotics may prevent unwanted CYP3A4 products. The evidence to explain the comprehensive biotransformation of major compounds from Centella asiatica and Orthosiphon stamineus is inadequate. The aim of the present study was to determine the specific interaction between CYP3A4 ferric–oxidative active sites and potential SOMs for the major chemical compounds of C. asiatica and O. stamineus. Molecular docking on CYP3A4 ferric–oxo (bound to the protoporphirin group, HEME–Fe3+–O-) was carried out using the CDOCKER simulation program to predict the SOMs for compounds from C. asiatica (asiaticoside, madecassoside, asiatic acid and madecassic acid) and O. stamineus (sinensetin, eupatorin and 5-hydroxy-6,7,3',4'-tetramethoxyflavone (5TMF)). Binding energies, residue–ligand interactions, and SOMs were obtained from the analysis. The molecular docking results also revealed that sinensetin, eupatorin, and 5TMF bound strongly to the CYP3A4 active site with binding energies of -22.44, -34.29, and -25.84 kcal/mol, respectively. Generally, the residues Arg106, Ile301, Ther309, Glu374 and Ala307 were identified to have the highest number of interactions with eupatorine, 5TMF and sinensetin. The SOM prediction for eupatorine showed interactions between the oxygen of the HEME iron (ferric oxo) and the C-11 and O-4 atoms. The possible metabolism reactions were C-11-hydroxylation and O-4-demethylation. For 5TMF, the SOM prediction for interactions were at the C-13 and O-7 positions, which could undergo hydroxylation and O-demethylation reactions, respectively. The SOM of sinensetin was predicted at C-3’ and the possible metabolic reaction taking place would be hydroxylation. The present study concluded that the major compounds of O. stamineus have the potential to be metabolized by CYP3A4 through hydroxylation and O-demethylation reactions. These data may be useful for phytomedicine product development related to CYP3A4 biotransformation mechanisms.

Biological treatment of refractory pollutants in industrial wastewaters under aerobic or anaerobic condition: Batch tests and associated microbial community analysis

In this study, aerobic or anaerobic biological treatment of streams collected from different units of industrial wastewater treatment plant (WWTP) was studied in a series of batch tests. Under aerobic condition, the removal efficiencies of COD, NH4+-N and TP were 57.7%, 83.8% and 100% for influent of WWTP (IN), 64.4%, 61.3% and 100% for effluent of secondary sedimentation tank (EN-SST), and 2.3%, 64.3% and 10.6% for effluent of advanced oxidation tank (EN-AOT). Meanwhile, the removal efficiencies of COD, NH4+-N, TOC were above 30% under anaerobic conditions. The GC–MS analysis showed a presence of 59 kinds of chemicals in IN, 28 in EN-SST, and 8 in EN-AOT. The main organic compounds were long-chain alkanes and derivatives. After aerobic/anaerobic biological treatment, the abundance of Proteobacteria, Bacteroidota, Nitrospirota was 40.4–56.1% (IN), 5.3–17.5% (EN-SST), and 4.6–13.4% (EN-AOT), respectively. This work contributed to deeply understanding the biotransformation mechanisms of refractory pollutants in industrial wastewaters.

Temporal exposure to malathion: Biochemical changes in the Amazonian fish tambaqui, Colossoma macropomum.

The main toxicity mechanism of organophosphate insecticides such as malathion is the acetylcholinesterase enzyme inhibition. However, fish responses to organophosphates may vary depending on the activation of different defense mechanisms as well as the length of exposure. As such, the evaluation of acetylcholinesterase activity, in combination with the evaluation of biotransformation and antioxidants enzymes levels, is useful for indicating damage in fish exposed to this insecticide. Moreover, evaluating mitochondrial activity might evidence how the hierarchic responses occur in relation to the length of time that the fish is exposed. Therefore, the aim of our study is to evaluate whether the length of exposure to malathion differentially affects the biochemical responses of tambaqui. Our hypothesis is that the physiological alterations due to exposure are time dependent. Fish were exposed to sublethal concentrations of the insecticide during 6, 12, 24, 36, and 48h. Contrary to expectations, there was no acetylcholinesterase activity inhibition during the experiment, which indicates an absence of neurotoxicity. Phase II biotransformation mechanism was activated early, especially in the liver. Oxidative damage was evident in the first hours of exposure and was concurrent with the activation of antioxidant enzymes. Mitochondrial bioenergetics were differentially affected by the length of exposure. The data suggest that the tambaqui regulates mitochondrial respiration differently over time, seeking to maintain homeostasis and ATP demand, and ensures the activation of response mechanisms, thus minimizing oxidative damage and avoiding the neurotoxicity of malathion.

Arsenic Biotransformation: It is a complex process

Arsenic Biotransformation: It is a complex process

Golden Gate Assembly of Aerobic and Anaerobic Microbial Bioreporters.

Microbial bioreporters provide direct insight into cellular processes by producing a quantifiable signal dictated by reporter gene expression. The core of a bioreporter is a genetic circuit in which a reporter gene (or operon) is fused to promoter and regulatory sequences that govern its expression. In this study, we develop a system for constructing novel Escherichia coli bioreporters based on Golden Gate assembly, a synthetic biology approach for the rapid and seamless fusion of DNA fragments. Gene circuits are generated by fusing promoter and reporter sequences encoding yellow fluorescent protein, mCherry, bacterial luciferase, and an anaerobically active flavin-based fluorescent protein. We address a barrier to the implementation of Golden Gate assembly by designing a series of compatible destination vectors that can accommodate the assemblies. We validate the approach by measuring the activity of constitutive bioreporters and mercury and arsenic biosensors in quantitative exposure assays. We also demonstrate anaerobic quantification of mercury and arsenic in biosensors that produce flavin-based fluorescent protein, highlighting the expanding range of redox conditions that can be examined by microbial bioreporters. IMPORTANCE Microbial bioreporters are versatile genetic tools with wide-ranging applications, particularly in the field of environmental toxicology. For example, biosensors that produce a signal output in the presence of a specific analyte offer less costly alternatives to analytical methods for the detection of environmental toxins such as mercury and arsenic. Biosensors of specific toxins can also be used to test hypotheses regarding mechanisms of uptake, toxicity, and biotransformation. In this study, we develop an assembly platform that uses a synthetic biology technique to streamline construction of novel Escherichia coli bioreporters that produce fluorescent or luminescent signals either constitutively or in response to mercury and arsenic exposure. Beyond the synthesis of novel biosensors, our assembly platform can be adapted for numerous applications, including labeling bacteria for fluorescence microscopy, developing gene expression systems, and modifying bacterial genomes.

Distribution and speciation of arsenic in seasonally stratified reservoirs: Implications for biotransformation mechanisms governing interannual variability

HPLC-ICPMS was used to analyze the spatiotemporal variation of As species in different sections and tributaries of the Aha Reservoir over four seasons, and the migration and transformation mechanisms were clarified by combined analysis of hydrochemical parameters and microbial composition. The results showed that the internal release of As from the reservoir sediments is mainly due to the reduction of iron oxide and the release of adsorbed As(V). The average proportion of As(III) increased from 27.2% in autumn to 46.5% in summer, 68.9% in winter, and up to 70.8% in spring. In spring and summer, the high concentration of As(III) and organic arsenic in the epilimnion under phosphorus restriction was caused by the reductive metabolism of phytoplankton after intake of As(V). The arsenic species in the metalimnion were mainly affected by the oxidation-reduction potential (ORP). In summer and autumn, As-oxidizing bacteria used As(III) as an electron donor, and nitrate played an important role as an electron acceptor, maintaining the dominance of As(V) in the hypolimnion. However, in winter and spring, temperature-controlled ORP was the main process, which was dominated by As(III). In conclusion, As species show annual cycles in different layers of seasonally thermal stratified reservoirs. It provides a systematic mechanism of As species transformation in reservoirs, especially the effect of biological transformation mechanism.