A new bacterium, Rhodococcus sp. S2-17, which could completely degrade an emerging organic pollutant, benzophenone-3 (BP-3), was isolated from contaminated sediment through an enrichment procedure, and its BP-3 catabolic pathway and genes were identified through metabolic intermediate and transcriptomic analyses and biochemical and genetic studies. Metabolic intermediate analysis suggested that strain S2-17 may degrade BP-3 using a catabolic pathway progressing via the intermediates BP-1, 2,4,5-trihydroxy-benzophenone, 3-hydroxy-4-benzoyl-2,4-hexadienedioic acid, 4-benzoyl-3-oxoadipic acid, 3-oxoadipic acid, and benzoic acid. A putative BP-3 catabolic gene cluster including cytochrome P450, flavin-dependent oxidoreductase, hydroxyquinol 1,2-dioxygenase, maleylacetate reductase, and α/β hydrolase genes was identified through genomic and transcriptomic analyses. Genes encoding the cytochrome P450 complex that demethylates BP-3 to BP-1 were functionally verified through protein expression, and the functions of the other genes were also verified through knockout mutant construction and intermediate analysis. This study suggested that strain S2-17 might have acquired the ability to catabolize BP-3 by recruiting the cytochrome P450 complex and α/β hydrolase, which hydrolyzes 4-benzoyl-3-oxoadipic acid to benzoic acid and 3-oxoadipic acid, genes, providing insights into the recruitment of genes of for the catabolism of emerging organic pollutants.

Despite publication of numerous of papers, the effects of fluoxetine on fish behaviour remains mired in controversy and contradiction. One reason for this controversy is that fluoxetine displays distinct and opposing acute and chronic effects. A second reason is that most studies have been limited to two or at the most three concentrations. To address these deficiencies we exposed adult zebrafish, both single females and shoals consisting of one male and two females, to seven fluoxetine concentrations, ranging from 5 ng/L to 5 μg/L and measured their swimming behaviour, and response to a conspecific alarm substance (CAS) at seven, 14 and 28 days. We also measured the light startle response of unexposed F1 larvae at days seven and 28 post-hatch and the response to CAS at day 28. On day 7 fluoxetine decreased swimming speed at concentrations ≥500 ng/L. After addition of CAS fish exposed to 5, 500 and 1000 ng/L decreased swimming, while fish exposed to 10, 500 and 1000 ng/L significantly increased time motionless. On day 14 only fish exposed to 50 ng/L were significantly slower than controls before addition of CAS, but afterwards fish exposed to 5, 50, 1000 and 5000 ng/L showed significant differences from controls. On day 28 fish exposed to 50 and 5000 ng/L had slower average swimming speeds than controls before addition of CAS. After addition all fish except controls and those exposed to 500 ng/L showed decreased average speed. At seven days post-hatch, F1 larvae whose parents were exposed to 100 ng/L showed significantly higher activity than controls and those exposed to 500 ng/L fluoxetine showed lower activity in the light startle response. This study shows that the effects of fluoxetine vary with time and also in a non-monotonic manner. We suggest that the complex nature of the serotonergic system with multilateral effects at the genomic, biochemical and physiological levels interacting with environmental stimuli result in non-linear dose-response behavioural patterns.

Numerous recent studies have underlined the crucial players of noncoding RNAs (ncRNAs), i.e., microRNAs(miRNAs), long noncoding RNAs(lncRNAs) and circle RNAs(circRNAs) participating in genotoxic responses induced by a wide variety of environmental genotoxicants consistently. Genotoxic-derived ncRNAs provide us a new epigenetic molecular–ecological network (MEN) insights into the underlying mechanisms regarding genotoxicant exposure and genotoxic effects, which can modify ncRNAs to render them “genotoxic” and inheritable, thus potentially leading to disease risk via epigenetic changes. In fact, the spatial structures of ncRNAs, particularly of secondary and three-dimensional structures, diverse environmental genotoxicants as well as RNA splicing and editing forma dynamic pool of ncRNAs, which constructs a MEN in cells together with their enormous targets and interactions, making biological functions more complicated. We nonetheless suggest that ncRNAs have both beneficial(positive) and harmful(negative) effects, i.e., are “double-edged” in regulating genotoxicant toxic responses. Understanding the “double-edged” effects of ncRNAs is of crucial importance for our further comprehension of the pathogenesis of human diseases induced by environmental toxicants and for the construction of novel prevention and therapy targets. Furthermore, the MEN formed by ncRNAs and their interactions each other as well as downstream targets in the cells is important for considering the active relationships between external agents (environmental toxicants) and inherent genomic ncRNAs, in terms of suppression or promotion (down- or upregulation), and engineered ncRNA therapies can suppress or promote the expression of inherent genomic ncRNAs that are targets of environmental toxicants. Moreover, the MEN would be expected to be would be applied to the mechanistic explanation and risk assessment at whole scene level in environmental genotoxicant exposure. As molecular biology evolves rapidly, the proposed MEN perspective will provide a clearer or more comprehensive holistic view.

Dibenzofuran (DBF) derivatives have caused serious environmental problems, especially those produced by paper pulp bleaching and incineration processes. Prominent for its resilient mutagenicity and toxicity, DBF poses a major challenge to human health. In the present study, a new strain of Pseudomonas aeruginosa, FA-HZ1, with high DBF-degrading activity was isolated and identified. The determined optimum conditions for cell growth of strain FA-HZ1 were a temperature of 30 °C, pH 5.0, rotation rate of 200 rpm and 0.1 mM DBF as a carbon source. The biochemical and physiological features as well as usage of different carbon sources by FA-HZ1 were studied. The new strain was positive for arginine double hydrolase, gelatinase and citric acid, while it was negative for urease and lysine decarboxylase. It could utilize citric acid as its sole carbon source, but was negative for indole and H2S production. Intermediates of DBF 1,2-dihydroxy-1,2-dihydrodibenzofuran, 1,2-dihydroxydibenzofuran, 2-hydroxy-4-(3′-oxo-3′H-benzofuran-2′-yliden)but-2-enoic acid, 2,3-dihydroxybenzofuran, 2-oxo-2-(2′-hydrophenyl)lactic acid, and 2-hydroxy-2-(2′-hydroxyphenyl)acetic acid were detected and identified through liquid chromatography-mass analyses. FA-HZ1 metabolizes DBF by both the angular and lateral dioxygenation pathways. The genomic study identified 158 genes that were involved in the catabolism of aromatic compounds. To identify the key genes responsible for DBF degradation, a proteomic study was performed. A total of 1459 proteins were identified in strain FA-HZ1, of which 100 were up-regulated and 104 were down-regulated. A novel enzyme “HZ6359 dioxygenase”, was amplified and expressed in pET-28a in E. coli BL21(DE3). The recombinant plasmid was successfully constructed, and was used for further experiments to verify its function. In addition, the strain FA-HZ1 can also degrade halogenated analogues such as 2, 8-dibromo dibenzofuran and 4-(4-bromophenyl) dibenzofuran. Undoubtedly, the isolation and characterization of new strain and the designed pathways is significant, as it could lead to the development of cost-effective and alternative remediation strategies. The degradation pathway of DBF by P. aeruginosa FA-HZ1 is a promising tool of biotechnological and environmental significance.

Exposure to pesticides results in DNA damage and genomic instability. We previously predicted that endosulfan might be associated with leukemia, but the role of endosulfan in leukemia cells has been unexplored. The aim of this study is to elucidate molecular mechanism of endosulfan-induced DNA damage response in human leukemia cells. We performed endosulfan exposure experiments in K562 cells with varying concentrations of endosulfan for 48 h and found that endosulfan lowered cell viability in a dose-dependent manner. We observed the dramatic DNA damage using comet assay and the increase of micronucleus in 75 μM endosulfan-exposed cells. Endosulfan at 75 μM caused the expression alterations of ATM and DNA repair genes such as FANCD2, and BRCA1/2 at different exposure time points (12, 24, 48 h), which was reversed by ATM inhibitor KU-55933. Endosulfan significantly increased the mRNA expression levels of p53 and GADD45A, and decreased PCNA and XRCC2 at 48 h after exposure. Flow cytometric analysis showed that endosulfan at 50 and 75 μM induced cell cycle G1 arrest, a response attributed to down-regulation of CDK6 and up-regulation of p21. We also observed that endosulfan at 50 and 75 μM induced a considerable percentage of cells to undergo apoptosis, as detected by Annexin-V binding assays. Endosulfan resulted in the activation of caspase-3, and elevated the expression levels of PUMA and the ratio of BAX/Bcl-2. These findings suggest that endosulfan caused DNA damage response throughATM-p53 signaling pathway, implicating the potential correlation between endosulfan and leukemia.

Lipids are the main energy support during gametogenesis. Digestive gland is the key organ of aquatic animal metabolism for storing nutrition and supplying energy. It participates in a variety of life activities (such as growth, digestion, immunity, and reproduction). Nutrients stored in digestive glands, especially lipids, provide energy for reproductive behaviors such as gametogenesis and ovulation. A large number of studies have confirmed the accumulation of lipids from digestive gland to gonad during gametogenesis. At present, the research on the interference mechanism of persistent organic pollutants (POPs) on lipid metabolism of aquatic animals and the adaptive response of aquatic animals to POPs stress focus on biochemical levels or a few genes. The potential molecular mechanism of lipid metabolism interference needs to be further studied. In addition, as an important stage of aquatic animals, the reproductive period is a vigorous period of lipid metabolism. However, at present, there is no report on the molecular mechanism of POPs interfering with the lipid metabolism of the digestive gland in the reproductive process of aquatic animals. In this study, female scallop C. farreri was cultured in natural seawater and exposed to 4 μg/L B[a]P in seawater. Transcriptome analysis of digestive glands at multiple stages (proliferative stage, growth stage, mature stage and spawn stage) was performed, and iPath pathway analysis was used to analyze lipid metabolism pathways and differential genes. The interference mechanism of lipid metabolism in bivalves during reproductive period was revealed. This study will provide valuable genomic information on the role of digestive glands in lipid metabolism and reproduction of C. farreri, and will contribute to further functional genomics of bivalves and other closely related species.

Dichlorodiphenyltrichloroethane (DDT) poses a significant health risk to humans which is associated with genomic DNA hypomethylation. However, the mechanism and biological consequences remain poorly understood. In vitro assays confirmed that the DDT metabolites 2,2-bis(p-chlorophenyl)-acetic acid (DDA) and 1-chloro-2,2-bis-(p-chlorophenyl)ethylene (DDMU), but not other DDT metabolites, significantly inhibited DNA methyltransferase 1 (DNMT1) activity, leading to genomic hypomethylation in cell culture assays. DNMT1 as a target for DNA hypomethylation induced by DDT metabolites was also confirmed using cell cultures in which DNMT1 was silenced or highly expressed. DDA and DDMU can modify methylation markers in the promoter regions of sexual development-related genes, and change the expression of Sox9 and Oct4 in embryonic stem cells. Molecular docking indicated that DDA and DDMU bound to DNMT1 with high binding affinity. Molecular dynamic simulation revealed that DDA and DDMU acted as allosteric modulators that reshaped the conformation of the catalytic domain of DNMT1. These findings provide a new insight into DDT-induced abnormalities in sexual development and demonstrate that selective binding to DNMT1 by DDA and DDMU can interfere with human DNMT1 activity and regulate the expression of the Sox9 and Oct4 genes.

The present study aimed to show that nickel and fluoride exhibited synchronized co-inhibited uptake in the aromatic rice cultivar, Gobindobhog, since bioaccumulation of the two elements was lower than that during individual stress, so that overall growth under combined stress was similar to control seedlings. On the contrary, lead and fluoride stimulated their co-uptake which triggered oxidative damages, NADPH oxidase activity, methylglyoxal accumulation, photosynthetic inhibition, membrane-protein damages, necrosis and genomic template degradation. Accumulation of proline, anthocyanins, non-protein thiols and phytochelatins was stimulated for systemic protection against reactive oxygen species (ROS) and xenobiotic-mediated injuries during lead-fluoride toxicity. ROS accumulation during nickel-fluoride stress was insignificant due to which enhanced accumulation of most antioxidants was not required. Glutathione depletion during combined lead-fluoride toxicity was due to its utilization in the glyoxalase cycle and also inhibition of glutathione reductase. However, the nickel-fluoride-treated sets maintained glutathione reserves and glyoxalase activity similar to those in control. Presence of fluoride ‘safeguarded’ the glutathione-utilizing enzymes like glutathione reductase, glutathione peroxidase and glutathione-S-transferase during dual lead-fluoride stress. This was because these enzymes showed higher activity compared to that under lead toxicity alone. Enzymatic antioxidants like superoxide dismutase, ascorbate peroxidase and guaiacol peroxidase were activated during lead-fluoride toxicity due to altered iron and copper homeostasis. Catalase activity was strongly inhibited, resulting in the inability to scavenge H₂O₂ and suppression of the fluoride-adaptable phenotype. However, none of the enzymatic antioxidants were inhibited during nickel-fluoride stress, which cumulatively allowed the seedlings to maintain normal physiology. Overall our findings holistically reveal the physiological plasticity of Gobindobhog in response to two different heavy metals under the influence of fluoride.

Fipronil, a broad-spectrum chiral insecticide, has been documented to induce significant neurotoxicity to nontarget aquatic species; however, whether its neurotoxicity behaves enantioselectively and what molecular mechanisms correspond to the neurotoxicity remain unanswered. To date, few investigations have focused on the genomic mechanisms responsible for the enantioselective toxicity of chiral pesticides. The epigenetic modifications, especially DNA methylation, caused by the pesticides are also blind spot of the research works. Video tracking showed that R-fipronil exhibited more intense neurotoxicity, as well as the induction of more severe anxiety-like behavior, such as boosted swimming speed and dysregulated photoperiodic locomotion, to embryonic and larval zebrafish compared with S-fipronil. The MeDIP-Seq analysis, combined with Gene Ontology and KEGG, revealed that R-fipronil disrupted five signaling pathways (MAPK, Calcium signaling, Neuroactive ligand-receptor interaction, Purine metabolism, and Endocytosis) to a greater extent than S-fipronil through the hypermethylation of several important neuro-related genes, whereas no significant alterations of global DNA methylation were observed on the two enantiomers. To summarize, our data indicated that the fipronil-conducted enantioselective neurotoxicity likely applied its enantioselectivity by the dysregulation of DNA methylation. Our study also provided novel epigenetic insights into the study of enantioselective biological effects and the relevant underlying mechanisms of chiral insecticide.

Estrogenic endocrine disrupting chemicals (EDCs) are natural hormones, synthetic compounds or industrial chemicals that mimic estrogens due to their structural similarity with estrogen's functional moieties. They typically enter aquatic environments through wastewater treatment plant effluents or runoff from intensive livestock operations. Globally, most natural and synthetic estrogens in receiving aquatic environments are in the low ng/L range, while industrial chemicals (such as bisphenol A, nonylphenol and octylphenol) are present in the μg to low mg/L range. These environmental concentrations often exceed laboratory-based predicted no effect concentrations (PNECs) and have been evidenced to cause negative reproductive impacts on resident aquatic biota. In vertebrates, such as fish, a well-established indicator of estrogen-mediated endocrine disruption is overexpression of the egg yolk protein precursor vitellogenin (Vtg) in males. Although the vertebrate Vtg has high sensitivity and specificity to estrogens, and the molecular basis of its estrogen inducibility has been well studied, there is growing ethical concern over the use of vertebrate animals for contaminant monitoring. The potential utility of the invertebrate Vtg as a biomonitor for environmental estrogens has therefore gained increasing attention. Here we review evidence providing support that the molluscan Vtg holds promise as an invertebrate biomarker for exposure to estrogens. Unlike vertebrates, estrogen signalling in invertebrates remains largely unclarified and the classical genomic pathway only partially explains estrogen-mediated activation of Vtg. In light of this, in the latter part of this review, we summarise recent progress towards understanding the molecular mechanisms underlying the activation of the molluscan Vtg gene by estrogens and present a hypothetical model of the interplay between genomic and non-genomic pathways in the transcriptional regulation of the gene.