Triphenyltin degradation and proteomic response by an engineered Escherichia coli expressing cytochrome P450 enzyme

Temporal and Within-Sporophyte Variations in Triphenyltin Chloride (TPTCL) and Its Degradation Products in Cultivated Undaria pinnatifida

Undaria pinnatifida can effectively deal with organotin pollution through its excellent accumulation and degradation capabilities found under laboratory conditions. However, nothing is known regarding its accumulation, degradation performance, and related impact factors in the wild farming area. In this study, we monitored triphenyltin chloride (TPTCL) contents and degradation products in different algal parts (blades, stipes, sporophylls, and holdfasts) of cultivated U. pinnatifida from December 2018 to May 2019. Our results showed that sporophytes had an accumulation and degradation capacity for TPTCL. The TPTCL contents and degradation products varied with the algal growth stages and algal parts. TPTCL accumulated in the blades at the growth stage and the blades, stipes, sporophylls, and holdfasts at the mature stage. The TPTCL content among algal parts was blades (74.92 ± 2.52 μg kg-1) > holdfasts (62.59 ± 1.42 μg kg-1) > sporophylls (47.24 ± 1.41 μg kg-1) > stipes (35.53 ± 0.55 μg kg-1). The primary degradation product DPTCL accumulated only in the blades at any stage, with a concentration of 69.30 ± 3.89 μg kg-1. The secondary degradation product MPTCL accumulated in the blades at the growth stage and in the blades, stipe, and sporophyll at the mature stage. The MPTCL content among algal parts was blades (52.80 ± 3.48 μg kg-1) > sporophylls (31.08 ± 1.53 μg kg-1) > stipes (20.44 ± 0.85 μg kg-1). The accumulation pattern of TPTCL and its degradation products seems closely related to nutrient allocation in U. pinnatifida. These results provide the basis for applying cultivated U. pinnatifida in the bioremediation of organotin pollution and the food safety evaluation of edible algae.

New roles for Bacillus thuringiensis in the removal of environmental pollutants

For a long time, the well-known Gram-positive bacterium Bacillus thuringiensis (Bt) has been extensively studied and developed as a biological insecticide for Lepidoptera and Coleoptera pests due to its ability to secrete a large number of specific insecticidal proteins. In recent years, studies have found that Bt strains can also potentially biodegrade residual pollutants in the environment. Many researchers have isolated Bt strains from multiple sites polluted by exogenous compounds and characterized and identified their xenobiotic-degrading potential. Furthermore, its pathway for degradation was also investigated at molecular level, and a number of major genes/enzymes responsible for degradation have been explored. At present, a variety of xenobiotics involved in degradation in Bt have been reported, including inorganic pollutants (used in the field of heavy metal biosorption and recovery and precious metal recovery and regeneration), pesticides (chlorpyrifos, cypermethrin, 2,2-dichloropropionic acid, etc.), organic tin, petroleum and polycyclic aromatic hydrocarbons, reactive dyes (congo red, methyl orange, methyl blue, etc.), and ibuprofen, among others. In this paper, the biodegrading ability of Bt is reviewed according to the categories of related pollutants, so as to emphasize that Bt is a powerful agent for removing environmental pollutants.

Deciphering the recent trends in pesticide bioremediation using genome editing and multi-omics approaches: a review

Pesticide pollution in recent times has emerged as a grave environmental problem contaminating both aquatic and terrestrial ecosystems owing to their widespread use. Bioremediation using gene editing and system biology could be developed as an eco-friendly and proficient tool to remediate pesticide-contaminated sites due to its advantages and greater public acceptance over the physical and chemical methods. However, it is indispensable to understand the different aspects associated with microbial metabolism and their physiology for efficient pesticide remediation. Therefore, this review paper analyses the different gene editing tools and multi-omics methods in microbes to produce relevant evidence regarding genes, proteins and metabolites associated with pesticide remediation and the approaches to contend against pesticide-induced stress. We systematically discussed and analyzed the recent reports (2015-2022) on multi-omics methods for pesticide degradation to elucidate the mechanisms and the recent advances associated with the behaviour of microbes under diverse environmental conditions. This study envisages that CRISPR-Cas, ZFN and TALEN as gene editing tools utilizing Pseudomonas, Escherichia coli and Achromobacter sp. can be employed for remediation of chlorpyrifos, parathion-methyl, carbaryl, triphenyltin and triazophos by creating gRNA for expressing specific genes for the bioremediation. Similarly, systems biology accompanying multi-omics tactics revealed that microbial strains from Paenibacillus, Pseudomonas putida, Burkholderia cenocepacia, Rhodococcus sp. and Pencillium oxalicum are capable of degrading deltamethrin, p-nitrophenol, chlorimuron-ethyl and nicosulfuron. This review lends notable insights into the research gaps and provides potential solutions for pesticide remediation by using different microbe-assisted technologies. The inferences drawn from the current study will help researchers, ecologists, and decision-makers gain comprehensive knowledge of value and application of systems biology and gene editing in bioremediation assessments.

Synthetization and characterization of SnCaAl2O3 nanocomposite and using as a superior adsorbent for Pb, Zn, and Cd ions in polluted water

The presence of heavy metals in drinking water or wastewater poses a serious threat to the ecosystem. Hence, the present study focused on synthesizing SnCaAl2O3 core-shell nanoparticles (C.N.P.s) in the α-Alumina phase by thermal annealing a stacked structure sandwiched between two Al2O3 layers at low temperatures. The obtained structure showed Sn N.P. floating gate with an Al2O3 dielectric stacked tunneling barrier to remove the excess of these heavy metals from polluted water. To characterize the prepared composites, X-ray diffraction (XRD), field emission scanning electron microscope (FE-SEM), and high-resolution transmission electron microscopy (HR-TEM) were used. The synthesized SnCaAl2O3 C.N.P.s composite was examined to utilize it as an adsorbent for removing Zn, Cd, and Pb divalent cations. The removal efficiency was studied by various parameters such as adsorbent dose, pH, contact time, metal concentrations, temperature, and coexisting ions. The experimental results were tested via Langmuir and Freundlich isotherm models. The obtained results were convenient to the Freundlich isotherm model. Moreover, the adsorption thermodynamic behavior of Zn+2, Cd+2, and Pb+2 on the synthesized composite was examined, and the process is endothermic and spontaneous under experimental conditions. The results illustrated that the adsorption efficiency of the SnCaAl2O3 core-shell nanoparticles (C.N.P.s) ranged from 88% to about 100% for all cations.

Biotechnological tools to elucidate the mechanism of pesticide degradation in the environment

Pesticides are widely used in agriculture, households, and industries; however, they have caused severe negative effects on the environment and human health. To clean up pesticide contaminated sites, various technological strategies, i.e. physicochemical and biological, are currently being used throughout the world. Biological approaches have proven to be a viable method for decontaminating pesticide-contaminated soils and water environments. The biological process eliminates contaminants by utilizing microorganisms' catabolic ability. Pesticide degradation rates are influenced by a variety of factors, including the pesticide's structure, concentration, solubility in water, soil type, land use pattern, and microbial activity in the soil. There is currently a knowledge gap in this field of study because researchers are unable to gather collective information on the factors affecting microbial growth, metabolic pathways, optimal conditions for degradation, and genomic, transcriptomic, and proteomic changes caused by pesticide stress on the microbial communities. The use of advanced tools and omics technology in research can bridge the existing gap in our knowledge regarding the bioremediation of pesticides. This review provides new insights on the research gaps and offers potential solutions for pesticide removal from the environment through the use of various microbe-mediated technologies.

Insights into biodegradation mechanisms of triphenyl phosphate by a novel fungal isolate and its potential in bioremediation of contaminated river sediment

In this study, Aspergillus sydowii FJH-1 isolated from soil was verified to be a novel triphenyl phosphate (TPhP) degrader. Biodegradation efficiency of TPhP by Aspergillus sydowii FJH-1 exceeded 90% within 6 days under the optimal conditions (pH 4-9, 30 ℃, initial concentration less than 20 mg/L). Proteomics analysis uncovered the proteins perhaps involved in hydrolysis, hydroxylation, methylation and sulfonation of TPhP and the primary intracellular adaptive responses of Aspergillus sydowii FJH-1 to TPhP stress. The expression of carboxylic ester hydrolase along with several thioredoxin- and glutathione-dependent oxidoreductases were induced to withstand the toxicity of TPhP. The presence of TPhP also caused obvious upregulation of proteins concerned with glycolysis, pentose phosphate pathway and tricarboxylic acid cycle. Data from toxicological tests confirmed that the cytotoxicity and phytotoxicity of TPhP was effectively decreased after treatment with Aspergillus sydowii FJH-1. Additionally, bioaugmentation with Aspergillus sydowii FJH-1 was available for promoting TPhP removal in real water and water-sediment system. Collectively, the present study offered a deeper insight into the biodegradation mechanism and pathway of TPhP by a newly screened fungal strain Aspergillus sydowii FJH-1 and validated the feasibility of applying this novel degrader in the bioremediation of TPhP-polluted matrices.

Bioremediation of triphenyl phosphate by Pycnoporus sanguineus: Metabolic pathway, proteomic mechanism and biotoxicity assessment

So far, no information about the biodegradability of TPhP by white rot fungi has previously been made available, herein, Pycnoporus sanguineus was used as the representative to investigate the potential of white rot fungi in TPhP bioremediation. The results suggested that the biodegradation efficiency of 5 mg/L TPhP by P. sanguineus was 62.84% when pH was adjusted to 6 and initial glucose concentration was 5 g/L. Seven biodegradation products were identified, indicating that TPhP was biotransformed through oxidative cleavage, hydroxylation and methylation. The proteomic analysis revealed that cytochrome P450s, aromatic compound dioxygenase, oxidizing species-generating enzymes, methyltransferases and MFS general substrate transporters might occupy important roles in TPhP biotransformation. Carboxylesterase and glutathione S-transferase were induced to resist TPhP stress. The biotreatment by P. sanguineus contributed to a remarkable decrease of TPhP biotoxicity. Bioaugmentation with P. sanguineus could efficiently promote TPhP biodegradation in the water-sediment system due to the cooperation between P. sanguineus and some putative indigenous degraders, including Sphingobium, Burkholderia, Mycobacterium and Methylobacterium. Overall, this study provided the first insights into the degradation pathway, mechanism and security risk assessment of TPhP biodegradation by P. sanguineus and verified the feasibility of utilizing this fungus for TPhP bioremediation applications.

iTRAQ-facilitated proteomic analysis of Bacillus cereus via degradation of malachite green

The wide use of malachite green (MG) as a dye has caused substantial concern owing to its toxicity. Bacillus cereus can against the toxic effect of MG and efficiently decolourise it. However, detailed information regarding its underlying adaptation and degradation mechanisms based on proteomic data is scarce. In this study, the isobaric tags for relative and absolute quantitation (iTRAQ)-facilitated quantitative method was applied to analyse the molecular mechanisms by which B. cereus degrades MG. Based on this analysis, 209 upregulated proteins and 198 downregulated proteins were identified with a false discovery rate of 1% or less during MG biodegradation. Gene ontology and KEGG analysis determined that the differentially expressed proteins were enriched in metabolic processes, catalytic activity, antioxidant activity, and responses to stimuli. Furthermore, real-time qPCR was utilised to further confirm the regulated proteins involved in benzoate degradation. The proteins BCE_4076 (Acetyl-CoA acetyltransferase), BCE_5143 (Acetyl-CoA acetyltransferase), BCE_5144 (3-hydroxyacyl-CoA dehydrogenase), BCE_4651 (Enoyl-CoA hydratase), and BCE_5474 (3-hydroxyacyl-CoA dehydrogenase) involved in the benzoate degradation pathway may play an important role in the biodegradation of MG by B. cereus. The results of this study not only provide a comprehensive view of proteomic changes in B. cereus upon MG loading but also shed light on the mechanism underlying MG biodegradation by B. cereus.

Bisphenol A degradation pathway and associated metabolic networks in Escherichia coli harboring the gene encoding CYP450

Although bisphenol A (BPA) can be transformed by CYP450, the metabolic networks involved in regulating the transformation processes are not clear. In this study, Escherichia coli harboring the gene encoding CYP450 was used as a model to elucidate the BPA degradation pathway and the associated metabolic network using a proteomic approach. The results showed that CYP450 promotes the transformation of BPA, generating 1,2-bis(4-hydroxyphenyl)-2-propanol and 2,2-bis(4-hydroxyphenyl)-1-propanol, with hydroquinone and 4-(2-hydroxypropan-2-yl)phenol formed in another pathway. The DNA adducts formed by 1,4-benzoquinone were reduced, and CYP450 played a positive role in cellular homeostasis by promoting the transformation of BPA and mismatch repair. An increase in the synthesis of cell membrane lipids was observed after dislodging BPA. BPA disturbed folate metabolism by decreasing the abundance of dihydrofolate reductase, which inhibited microbial metabolism in the absence of CYP450. The findings of this study revealed the molecular mechanism associated with the metabolic network responsible for pollutant tolerance and degradation.

Degradation of 2,2',4,4'-tetrabromodiphenyl ether by Pycnoporus sanguineus in the presence of copper ions

The degradation of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) by Pycnoporus sanguineus was investigated in order to explore the impact of the heavy metal Cu²⁺ on BDE-47 decomposition and the subsequent formation of metabolites, as well as to further elucidate the degradation mechanism of BDE-47. An increase in degradation rate from 18.63% to 49.76% in the first four days and its stabilization at (51.26 ± 0.08)% in the following days of BDE-47 incubation were observed. The presence of Cu²⁺ at 1 and 2 mg/L was found to promote the degradation rate to 56.41% and 60.79%, respectively, whereas higher level of Cu²⁺ (≥5 mg/L) inhibited the removal of BDE-47. The similar concentration effects of Cu²⁺ was also found on contents of fungal protein and amounts of metabolites. Both intracellular and extracellular enzymes played certain roles in BDE-47 transportation with the best degradation rate at 27.90% and 27.67% on the fourth and third day, individually. During the degradation of BDE-47, four types of hydroxylated polybrominated diphenyl ethers (OH-PBDEs), i.e., 6'-OH-BDE-47, 5'-OH-BDE-47, 4'-OH-BDE-17, 2'-OH-BDE-28, and two bromophenols, i.e., 2,4-DBP and 4-BP were detected and considered as degradation products. These metabolites were further removed by P. sanguineus at rates of 22.42%, 23.01%, 27.04%, 27.96%, 64.21%, and 40.62%, respectively.

Identification of novel pathways for biotransformation of tetrabromobisphenol A by Phanerochaete chrysosporium, combined with mechanism analysis at proteome level

The investigation of tetrabromobisphenol A (TBBPA) removal by Phanerochaete chrysosporium (P. chrysosporium) was conducted. Under optimal conditions (pH 5, inoculum size of 5% (v/v), initial glucose concentration of 5 g/L, TBBPA concentration of 5 mg/L), >97% of initial TBBPA was removed after 3 days. The TBBPA metabolites, tetrabromobisphenol A glycoside, tribromobisphenol A glycoside and monohydroxylated tetrabromobisphenol A, were identified for the first time by fungi transformation as being produced by glycosylation and oxidative hydroxylation, respectively. Proteome analysis showed that P. chrysosporium significantly upregulated cytochrome P450 monooxygenase, glutathione S-transferases, UDP-glucosyltransferase, O‑methyltransferase and other oxidoreductases for TBBPA oxidative hydroxylation, reductive debromination, glycosylation, O‑methylation and oxidative cleavage for detoxification. Data from cytotoxicity tests with human hepatocellular liver carcinoma (HepG2) confirmed that TBBPA toxicity was effectively decreased by P. chrysosporium treatment. Bioaugmentation with P. chrysosporium significantly improved the removal efficiency of TBBPA in water microcosms to 63.1% within 12 h. This study suggests that P. chrysosporium might be suitable for the removal of TBBPA from contaminated water.

Benzo(a)pyrene degradation by cytochrome P450 hydroxylase and the functional metabolism network of Bacillus thuringiensis

The relationship between benzo(a)pyrene biodegradation and certain target biomolecules has been investigated. To regulate the degradation process, the associated metabolism network must be clarified. To this end, benzo(a)pyrene degradation, carbon substrate metabolism and exometabolomic mechanism of Bacillus thuringiensis were analyzed. Benzo(a)pyrene was degraded through hydroxylation catalyzed by cytochrome P450 hydroxylase. After the treatment of 0.5 mg L^-1 of benzo(a)pyrene by 0.2 g L^-1 of cells for 9 d, biosorption and degradation efficiencies were measured at approximately 90% and 80%, respectively. During this process, phospholipid synthesis, glycogen, asparagine, arginine, itaconate and xylose metabolism were significantly downregulated, while glycolysis, pentose phosphate pathway, citrate cycle, amino sugar and nucleotide sugar metabolism were significantly upregulated. These findings offer insight into the biotransformation regulation of polycyclic aromatic hydrocarbons.

iTRAQ-based proteomic profiling of Pycnoporus sanguineus in response to co-existed tetrabromobisphenol A (TBBPA) and hexavalent chromium

In current study, we investigated the changes of proteome profiles of Pycnoporus sanguineus after a single exposure of Cr(VI), TBBPA and a combined exposure of TBBPA and Cr(VI), with the goal of illuminating the cellular mechanisms involved in the interactions of co-existed TBBPA and Cr(VI) with the cells of P. sanguineus at the protein level. The results revealed that some ATP-binding cassette (ABC) transporters were obviously induced by these pollutants to accelerate the transportation, transformation and detoxification of TBBPA and Cr(VI). Cr(VI) could inhibit the bioremoval of its organic co-pollutants TBBPA through suppressing the expression of several key proteins related to the metabolism of TBBPA by P. sanguineus, including two cytochrome P450s, pentachlorophenol 4-monooxygenase and glutathione S-transferases. Furthermore, Cr(VI) possibly reduced the cell vitality and growth of P. sanguineus by enhancing the expression of imidazole glycerol phosphate synthase as well as by decreasing the abundances of proteins associated with the intracellular metabolic processes, such as the tricarboxylic acid cycle, purine metabolism and glutathione biosynthesis, thereby adversely affecting the biotransformation of TBBPA. Cr(VI) also inhibited the expression of peptidyl prolyl cis/trans isomerases, thus causing the damage of cell membrane integrity. In addition, some important proteins participated in the resistance to Cr(VI) toxicity were observed to up-regulate, including heat shock proteins, 26S proteasome, peroxiredoxins and three critical proteins implicated in S-adenosyl methionine synthesis, which contributed to reducing the hazard of Cr(VI) to P. sanguineus. The results of this study provide novel insights into the physiological responses and molecular mechanism of white rot fungi P. sanguineus to the stress of concomitant TBBPA and Cr(VI).

Cellular metabolism network of Bacillus thuringiensis related to erythromycin stress and degradation

Erythromycin is one of the most widely used macrolide antibiotics. To present a system-level understanding of erythromycin stress and degradation, proteome, phospholipids and membrane potentials were investigated after the erythromycin degradation. Bacillus thuringiensis could effectively remove 77% and degrade 53% of 1 µM erythromycin within 24 h. The 36 up-regulated and 22 down-regulated proteins were mainly involved in spore germination, chaperone and nucleic acid binding. Up-regulated ribose-phosphate pyrophosphokinase and ribosomal proteins confirmed that the synthesis of protein, DNA and RNA were enhanced after the erythromycin degradation. The reaction network of glycolysis/gluconeogenesis was activated, whereas, the activity of spore germination was decreased. The increased synthesis of phospholipids, especially, palmitoleic acid and oleic acid, altered the membrane permeability for erythromycin transport. Ribose-phosphate pyrophosphokinase and palmitoleic acid could be biomarkers to reflect erythromycin exposure. Lipids, disease, pyruvate metabolism and citrate cycle in human cells could be the target pathways influenced by erythromycin. The findings presented novel insights to the interaction among erythromycin stress, protein interaction and metabolism network, and provided a useful protocol for investigating cellular metabolism responses under pollutant stress.