Transcriptome analysis of Rana chensinensis liver under trichlorfon stress

Isolation, identification and transcriptome analysis of triadimefon-degrading strain Enterobacter hormaechei TY18

Triadimefon, a type of triazole systemic fungicide, has been extensively used to control various fungal diseases. However, triadimefon could lead to severe environmental pollution, and even threatens human health. To eliminate triadimefon residues, a triadimefon-degrading bacterial strain TY18 was isolated from a long-term polluted site and was identified as Enterobacter hormaechei. Strain TY18 could grow well in a carbon salt medium with triadimefon as the sole nitrogen source, and could efficiently degrade triadimefon. Under triadimefon stress, a total of 430 differentially expressed genes (DEGs), including 197 up-regulated and 233 down-regulated DEGs, were identified in strain TY18 using transcriptome sequencing (RNA-Seq). Functional classification and enrichment analysis revealed that these DEGs were mainly related to amino acid transport and metabolism, carbohydrate transport and metabolism, small molecule and pyrimidine metabolism. Interestingly, the DEGs encoding monooxygenase and hydrolase activity acting on carbon-nitrogen were highly up-regulated, might be mainly responsible for the metabolism in triadimefon. Our findings in this work suggest that strain E. hormaechei TY18 could efficiently degrade triadimefon for the first time. They provide a great potential to manage triadimefon biodegradation in the environment successfully.

Cytochrome P450 superfamily in spotted sea bass: Genome-wide identification and expression profiles under trichlorfon and environmental stresses

Cytochrome P450s (CYPs), as one of the most diverse enzyme superfamilies in nature, play critical functions in antioxidant reactions against endogenous and exogenous compounds. In this study, we performed genome-wide characterization of CYP superfamily members and analyzed their expression patterns under several abiotic stresses in spotted sea bass, which is known as an economically important fish species in the Chinese aquaculture industry. A total of 55 CYP genes were identified and divided into 17 families within 10 clans. The analysis of phylogeny, gene structure, and syntenic relationships provided evidence for the evolution of CYP genes and confirmed their annotation and orthology. The expression of CYP genes was examined in the liver during trichlorfon stress using quantitative real-time PCR. The results showed that 20 tested CYP genes displayed significant mRNA expression changes, indicating that they may play crucial roles in the metabolism of trichlorfon and can be potential biomarkers for trichlorfon pollution. Moreover, by screening transcriptomic databases, 10, 3 and 19 CYP genes exhibited differential expression patterns in response to hypoxia, alkalinity and heat stress, respectively. Taken together, this study provided insights into the regulation of CYP genes by toxicological and environmental stresses, laid basis for extensive functional studies of the CYP superfamily in spotted sea bass and other teleost species.

Intestinal response of Rana chensinensis larvae exposed to Cr and Pb, alone and in combination

Although numerous investigations on the adverse impact of Cr and Pb have been performed, studies on intestinal homeostasis in amphibians are limited. Here, single and combined effects of Cr (104 μg/L) and Pb (50 μg/L) on morphological and histological features, bacterial community, digestive enzymes activities, as well as transcriptomic profile of intestines in Rana chensinensis tadpoles were assessed. Significant decrease in the relative intestine length (intestine length/snout-to-vent length, IL/SVL) was observed after exposure to Pb and Cr/Pb mixture. Intestinal histology and digestive enzymes activities were altered in metal treatment groups. In addition, treatment groups showed significantly increased bacterial richness and diversity. Tadpoles in treatment groups were observed to have differential gut bacterial composition from controls, especially for the abundance of phylum Proteobacteria, Firmicutes, Verrucomicrobia, Actinobacteria, and Fusobacteria as well as genus Citrobacter, Anaerotruncus, Akkermansia, and Alpinimonas. Moreover, transcriptomic analysis showed that the transcript expression profiles of GPx and SOD isoforms responded differently to Cr and/or Pb exposure. Besides, transcriptional activation of pro-apoptotic and glycolysis-related genes, such as Bax, Apaf 1, Caspase 3, PK, PGK, TPI, and GPI were detected in all treatment groups but downregulation of Bcl2 in Pb and Cr/Pb mixture groups. Collectively, these results suggested that Cr and Pb exposure at environmental relevant concentration, alone and in combination, could disrupt intestinal homeostasis of R. chensinensis tadpoles.

Copper-mediated shifts in transcriptomic responses of intestines in Bufo gargarizans tadpoles to lead stress

The differential transcriptomic responses of intestines in Bufo gargarizans tadpoles to Pb alone or in the presence of Cu were evaluated. Tadpoles were exposed to 30 μg/L Pb individually and in combination with Cu at 16 or 64 μg/L from Gosner stage (Gs) 26 to Gs 38. After de novo assembly, 105,107 unigenes were generated. Compared to the control group, 7387, 6937, and 11139 differentially expressed genes (DEGs) were identified in the treatment of Pb + Cu0, Pb + Cu16, and Pb + Cu64, respectively. In addition, functional annotation and enrichment analysis of DEGs revealed substantial transcriptional reprogramming of diverse molecular and biological pathways were induced in all heavy metal treatments. The relative expression levels of genes associated with intestinal epithelial barrier and bile acids (BAs) metabolism, such as mucin2, claudin5, ZO-1, Asbt, and Ost-β, were validated by qPCR. This study demonstrated that Pb exposure induced transcriptional responses in tadpoles, and the responses could be modulated by Cu.

PDIA6 involves the thermal stress response of razor clam, Sinonovacula constricta

Protein disulfide isomerases A6 (PDIA6), an oxidoreductase and isomerase, catalyzes the oxidation reduction and isomerization of disulfide bonds, and serves as molecular chaperone to prevent the buildup of misfolded proteins under various environmental insults. However, the role of PDIA6 in mollusks remains largely obscure, although its multifunctional protein has been reported in other species under adverse conditions. To fill this gap, we identified PDIA6 from the razor clam Sinonovacula constricta (ScPDIA6) and investigated its expression patterns in response to thermal stress. Tissue distribution showed that the mRNA transcript of ScPDIA6 was ubiquitously expressed in nine tested tissues. Temporal expression profiles by qPCR revealed that ScPDIA6 in the gill and mantle was significantly increased by hyper-thermic treatment. Further, Western blot and immunofluorescence indicated that ScPDIA6 was significantly upregulated by thermal treatment at the protein level. Additionally, the survival test demonstrated that the viability of E. coli cells expressing recombinant ScPDIA6 protein increased at 42 °C compared with empty vector. Overall, these findings suggested that ScPDIA6 may play a pivotal role in counteracting thermal stress. This study will provide valuable reference data resource for understanding the potential role of PDIA6 in mollusks.

Effects of isolated and combined exposures of Boana curupi (Anura: Hylidae) tadpoles to environmental doses of trichlorfon and ultraviolet radiation

The biodiversity collapse strongly affects the amphibian group and many factors have been pointed out as catalytic agents. It is estimated that several events in the amphibian population decline worldwide may have been caused by the interaction of multiple drivers. Thus, this study aimed to evaluate the stressful effects of the exposure to environmental doses of trichlorfon (TCF) pesticide (0.5 μg/L; and an additional 100-fold concentration of 50 µg/L) and ultraviolet radiation (UV) (184.0 kJ/m² of UVA and 3.4 kJ/m² of UVB, which correspond to 5% of the daily dose) in tadpoles of the Boana curupi species (Anura: Hylidae). The isolated and combined exposures to TCF happened within 24 h of acute treatments under laboratory-controlled conditions. In the combined treatments, we adopted three different moments (M) of tadpole irradiation from the beginning of the exposures to TCF (0 h - M1; 12 h - M2; and 24 h - M3). Then, we evaluated tadpole survival, change in morphological characters, induction of apoptotic cells, lipid peroxidation (LPO), protein carbonyl content (PCC), glutathione S-transferase (GST), non-protein thiols (NPSH), and acetylcholinesterase (AChE), as well as the induction of genomic DNA (gDNA) damage. UVB treatment alone resulted in high mortality, along with a high level of apoptosis induction. Both UVA, UVB, and TCF increased LPO, PC, and AChE, while decreased GST activity. Regarding co-exposures, the most striking effect was observed in the interaction between UVB and TCF, which surprisingly decreased UVB-induced tadpole mortality, apoptosis, and gDNA damage. These results reinforce the B. curupi sensitivity to solar UVB radiation and indicate a complex response in face of UVB interaction with TCF, which may be related to activation of DNA repair pathways and/or inhibition of apoptosis, decreasing UVB-induced tadpole mortality.

Hypothesis-driven dragging of transcriptomic data to analyze proven targeted pathways in Rhinella arenarum larvae exposed to organophosphorus pesticides

Transcriptional analysis of the network of transcription regulators and target pathways in exposed organisms may be a hard task when their genome remains unknown. The development of hundreds of qPCR assays, including primer design and normalization of the results with the appropriate housekeeping genes, seems an unreachable task. Alternatively, we took advantage of a whole transcriptome study on Rhinella arenarum larvae exposed to the organophosphorus pesticides azinphos-methyl and chlorpyrifos to evaluate the transcriptional effects on a priori selected groups of genes. This approach allowed us to evaluate the effects on hypothesis-selected pathways such as target esterases, detoxifying enzymes, polyamine metabolism and signaling, and regulatory pathways modulating them. We could then compare the responses at the transcriptional level with previously described effects at the enzymatic or metabolic levels to obtain global insight into toxicity-response mechanisms. The effects of both pesticides on the transcript levels of these pathways could be considered moderate, while chlorpyrifos-induced responses were more potent and earlier than those elicited by azinphos-methyl. Finally, we inferred a prevailing downregulation effect of pesticides on signaling pathways and transcription factor transcripts encoding products that modulate/control the polyamine and antioxidant response pathways. We also tested and selected potential housekeeping genes based on those reported for other species. These results allow us to conduct future confirmatory studies on pesticide modulation of gene expression in toad larvae.

De novo assembly and analysis of the transcriptome of the Siberian wood frog Rana amurensis

The Siberian wood frog Rana amurensis Boulenger, 1886 is the most hypoxia-tolerant amphibian. It can survive for several months in an almost complete absence of oxygen. Little is known about the mechanisms of this remarkable resilience, in part because studies of amphibian genomes are impeded by their large size. To make the Siberian wood frog more amenable for genetic analysis, we performed transcriptome sequencing and de novo assembly for the R. amurensis brain under hypoxia and normoxia, as well as for the normoxic heart. In order to build a de novo transcriptome assembly of R. amurensis, we utilized 125-bp paired-end reads obtained from the brain under normoxia and hypoxia conditions, and from the heart under normoxia. In the transcriptome assembled from about 100,000,000 reads, 81.5 % of transcripts were annotated as complete, 5.3 % as fragmented, and 13.2 % as missing. We detected 59,078 known transcripts that clustered into 22,251 genes; 11,482 of them were assigned to specific GO categories. Among them, we found 6696 genes involved in protein binding, 3531 genes involved in catalytic activity, and 576 genes associated with transporter activity. A search for genes encoding receptors of the most important neurotransmitters, which may participate in the response to hypoxia, resulted in a set of expressed receptors of dopamine, serotonin, GABA, glutamate, acetylcholine, and norepinephrine. Unexpectedly, no transcripts for histamine receptors were found. The data obtained in this study create a valuable resource for studying the mechanisms of hypoxia tolerance in the Siberian wood frog, as well as for amphibian studies in general.

Transcriptome analysis reveals the molecular mechanism of long-term exposure of Eriocheir sinensis to low concentration of trichlorfon

Trichlorphon, a common organophosphorus pesticide (OPs), is widely used in aquaculture to prevent aquatic insects from infecting cultured objects as well as to control the excessive proliferation of plankton in water bodies. However, its repeated use time can contaminate water bodies and impart direct/indirect toxicity to beneficial aquatic species. However, the underlying mechanism regarding toxicity and cellular metabolism remains unclear. Understanding the mechanism would enable the standardized use and management of OPs and their use in the aquatic environment. Here, low concentration of trichlorphon (5 × 10^-5 g/L) was used to construct a hepatopancreatic transcriptional library 30 d, 60 d and 90 d after exposure using RNA-Seq. We detected 649, 148, and 2949 DEGs in the hepatopancreas of E. sinensis for the Tri01 vs. Ctr01, Tri02 vs. Ctr02 and Tri03 vs. Ctr03 library, respectively. The results of KEGG pathway enrichment analysis showed that DEGs were mainly enriched in signal transduction, carbohydrate metabolism, transport and catabolism, endocrine system, and digestive system. Also, under trichlorfon stress, DEGs of E. sinensis were enriched in thyroid hormone signaling pathways, protein digestion and absorption, cancer pathways, etc. The significant DEGs were mainly related to metabolism and the apoptosis and autophagy pathways. This study lays a foundation for further revealing the effects of long-term trichlorfon stress on E. sinensis as well as the potential physiological toxicity. The relevant transcriptome data could provide a reference for the molecular toxicological evaluation of trichlorfon in aquaculture.

Physarum polycephalum macroplasmodium exhibits countermeasures against TiO2 nanoparticle toxicity: A physiological, biochemical, transcriptional, and metabolic perspective

Concerns about the environmental and human health implications of TiO₂ nanoparticles (nTiO₂) are growing with their increased use in consumer and industrial products. Investigations of the underlying molecular mechanisms of nTiO₂ tolerance in organisms will assist in countering nTiO₂ toxicity. In this study, the countermeasures exhibited by the slime mold Physarum polycephalum macroplasmodium against nTiO₂ toxicity were investigated from a physiological, transcriptional, and metabolic perspective. The results suggested that the countermeasures against nTiO₂ exposure include gene-associated metabolic rearrangements in cellular pathways involved in amino acid, carbohydrate, and nucleic acid metabolism. Gene-associated nonmetabolic rearrangements involve processes such as DNA repair, DNA replication, and the cell cycle, and occur mainly when macroplasmodia are exposed to inhibitory doses of nTiO₂. Interestingly, the growth of macroplasmodia and mammal cells was significantly restored by supplementation with a combination of responsive metabolites identified by metabolome analysis. Taken together, we report a novel model organism for the study of nTiO₂ tolerance and provide insights into countermeasures taken by macroplasmodia in response to nTiO₂ toxicity. Furthermore, we also present an approach to mitigate the effects of nTiO₂ toxicity in cells by metabolic intervention.

Chronic trichlorfon stress induces differential transcriptome expression and interferes with multifunctional pathways in the brain of Rana chensinensis

Trichlorfon is widely used to control pest insects and various parasitic infestations in agriculture, aquaculture and human medicine. However, the long-term widespread use and overuse of trichlorfon poses risks to public and environmental health. Thus, the aim of this study was to evaluate the interference of trichlorfon on gene transcription patterns in the brain of Rana chensinensis with 4 weeks treatment under control conditions and 0.1 mg/L exposure. In total, 102,013 unigenes were obtained from the brain tissue of R. chensinensis, and 874 differentially expressed genes (DEGs) were identified. Functional annotation indicated that out of 118,643 unigenes, 45,600 (44.7%) were annotated in the Nr, Nt, the Swiss-Prot, KEGG, COG, and GO databases. The differential expression patterns of 4 genes associated with neural activity were selected and validated by quantitative polymerase chain reaction (qPCR). The results revealed that except for the canonical cholinesterase-based mechanism, trichlorfon could act on other receptors and alter certain types of neuronal ion channels as the major target sites. All of these effects ultimately cause disorders of multifunctional pathways and other neurotransmitter pathways in the host. The results further our understanding of the mechanisms underlying nontarget effects of organophosphate insecticides (OPs) through multitargets studies.

Impact of chronic exposure to trichlorfon on intestinal barrier, oxidative stress, inflammatory response and intestinal microbiome in common carp (Cyprinus carpio L.)

Trichlorfon is an organic phosphorus pesticide used to control different parasitic infections in aquaculture. The repeated, excessive use of trichlorfon can result in environmental pollution, thus affecting human health. This study aimed to determine the effects of different concentrations of trichlorfon (0, 0.1, 0.5 and 1.0 mg/L) on the intestinal barrier, oxidative stress, inflammatory response and intestinal microbiome of common carp. Trichlorfon exposure significantly reduced the height of intestinal villus and decreased the expression levels of tight junction genes, such as claudin-2, occludin and ZO-1, in common carp. Moreover, the activities of antioxidant enzymes, such as CAT, SOD and GSH-Px, exhibited a decreasing trend with increasing trichlorfon concentrations, while the contents of MDA and ROS elevated in the intestinal tissues of common carp. The mRNA and protein levels of pro-inflammatory cytokines TNF-α and IL-1β were significantly upregulated by trichlorfon exposure. The level of anti-inflammatory cytokine TGF-β was remarkably higher in 1.0 mg/L trichlorfon treatment group compared to control group. In addition, the results demonstrated that trichlorfon exposure could affect the microbiota community composition and decreased the community diversity in the gut of common carp. Notably, the proportions of some probiotic bacteria, namely, Lactobacillus, Bifidobacterium and Akkermansia, were observed to be reduced after trichlorfon exposure. In summary, the findings of this study indicate that exposure to different concentrations of trichlorfon can damage intestinal barrier, induce intestinal oxidative damage, trigger inflammatory reaction and alter gut microbiota structure in common carp.

Transcriptome and physiology analysis identify key metabolic changes in the liver of the large yellow croaker (Larimichthys crocea) in response to acute hypoxia

The large yellow croaker (Larimichthys crocea) is one of the most important marine economic fish in the southeast coast of China. However, hypoxia stress become a major obstacle to the benign development of L. crocea industry. To understand the energy metabolism mechanism adapted to hypoxia, we analyzed the transcriptome and physiology of L. crocea liver in response to hypoxia stress for different durations. We obtained 243,756,080 clean reads, of which 83.38% were successfully mapped to the reference genome of L. crocea. The heat map analysis showed that genes encoding enzymes involved in glycolysis/gluconeogenesis were significantly upregulated at various time points. Moreover, genes encoding enzymes related to the citrate cycle, oxidative phosphorylation, and amino acid metabolism were significantly downregulated at 6 and 24 h, but upregulated at 48 and 96 h. The change of liver in physiology processes, including respiratory metabolism, and activities of the carbohydrate metabolism enzymes showed a similar trend. The results revealed that the respiratory metabolism of L. crocea was mainly anaerobic within 24 h of hypoxia stress, and aerobic metabolism was dominant after 24 h. Carbohydrate metabolism plays a crucial role in energy supply and amino acid metabolism is an important supporting character to cope with acute hypoxia stress. There was no significant change in lipid utilization under short-term acute stress. This study increases our understanding of the energy metabolism mechanism of the hypoxia response in fish and provides a useful resource for L. crocea genetics and breeding.

Tissue Metabolism, Hematotoxicity, and Hepatotoxicity of Trichlorfon in Carassius auratus gibelio After a Single Oral Administration

Trichlorfon is a most widely used organophosphate insecticide in aquaculture, many successful results have been reported for bath treatments of trichlorfon to control parasites. However, immersion treatments of large stocks with trichlorfon has caused serious environmental pollution. In contrast, oral administration treatment has advantages on reducing environmental pollution and having little effect in non-targeted species. The aim of this study was to investigate the effect of trichlorfon on Carassius auratus gibelio physiology after a single oral administration. In this study, Carassius auratus gibelio was subjected to oral gavage with various concentrations of trichlorfon (0.5 g/kg, 1 g/kg, and 2 g/kg). The trichlorfon concentration in the plasma and liver tissue was quantified using liquid chromatography-tandem mass spectrometry at different time points. At the beginning of oral exposure, the uptake of trichlorfon in the plasma and liver tissue was fast, and trichlorfon was rapidly eliminated to a low level within 24 h. In addition, acetylcholinesterase, superoxide dismutase, catalase, and glutathione-S-transferase activities in the plasma and liver tissue changed significantly after trichlorfon exposure. Additionally, vacuolar degeneration, necrosis, and congestion of the central vein were observed in the liver after trichlorfon exposure, as assessed by hematoxylin and eosin staining. Our results suggested that trichlorfon could accumulate and induce hematotoxicity and hepatotoxicity in the plasma and liver tissue, the toxicity induced by trichlorfon might result in physiological disturbances in fish.