Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Functional categorization of transcriptome in the species Symphysodon aequifasciatus Pellegrin 1904 (Perciformes: Cichlidae) exposed to benzo[a]pyrene and phenanthrene

ABSTRACT: This study aims to evaluate the transcriptome alterations, through cDNA libraries, associated with the effects of the combination of two PAHs, benzo[a]pyrene (0.5M-NM-

ORGANISM(S): Symphysodon aequifasciata

SUBMITTER: Renato Lemgruber

PROVIDER: E-GEOD-51149 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Functional categorization of transcriptome in the species Symphysodon aequifasciatus Pellegrin 1904 (Perciformes: Cichlidae) exposed to benzo[a]pyrene and phenanthrene.

Lemgruber Renato de Souza Pinto Rde S Marshall Nislanha Ana dos Anjos NA Ghelfi Andrea A Fagundes Daniel Barros DB Val Adalberto Luis AL

PloS one 20131203 12

This study aims to evaluate the transcriptome alterations, through cDNA libraries, associated with the combined effects of two PAHs, benzo[a]pyrene (0.5 µg/L) and phenanthrene (50 µg/L), present in crude oil, on specimens of Symphysodon aequifasciatus (discus fish) after 48 h of exposure. The cDNA libraries were constructed according to the SOLiD™ SAGE™ protocol for sequencing in the SOLiD v.3 Plus sequencer. The results were analyzed by bioinformatics and differentially expressed genes were cat ...[more]

PMID: 24312524

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Project description:Background: Polycyclic aromatic hydrocarbons (PAHs) are toxic, widely-distributed, environmentally persistent, and carcinogenic byproducts of carbon-based fuel combustion. Previously, plant studies have shown that PAHs induce oxidative stress, reduce growth, and cause leaf deformation as well as tissue necrosis. To understand the transcriptional changes that occur during these processes, we performed microarray experiments on Arabidopsis thaliana L. under phenanthrene treatment, and compared the results to published Arabidopsis microarray data representing a variety of stress and hormone treatments. In addition, to probe hormonal aspects of PAH stress, we assayed transgenic ethylene-inducible reporter plants as well as ethylene pathway mutants under phenanthrene treatment. Results: Microarray results revealed numerous perturbations in signaling and metabolic pathways that regulate reactive oxygen species (ROS) and responses related to pathogen defense. A number of glutathione S-transferases that may tag xenobiotics for transport to the vacuole were upregulated. Comparative microarray analyses indicated that the phenanthrene response was closely related to other ROS conditions, including pathogen defense conditions. The ethylene-inducible transgenic reporters were activated by phenanthrene. Mutant experiments showed that PAH inhibits growth through an ethylene-independent pathway, as PAH-treated ethylene-insensitive etr1-4 mutants exhibited a greater growth reduction than WT. Further, phenanthrene-treated, constitutive ethylene signaling mutants had longer roots than the untreated control plants, indicating that the PAH inhibits parts of the ethylene signaling pathway. Conclusions: This study identified major physiological systems that participate in the PAH-induced stress response in Arabidopsis. At the transcriptional level, the results identify specific gene targets that will be valuable in finding lead compounds and engineering increased tolerance. Collectively, the results open a number of new avenues for researching and improving plant resilience and PAH phytoremediation. Arabidopsis thaliana (ecotype Columbia) plants were long-day grown with +/- 0.25 mM phenanthrene in sterile plates at 23C for 21d before harvest. At least 20 plants were pooled prior to each mRNA extraction.

Project description:Several environmental pollutants, especially organic compounds such as polycyclic aromatic hydrocarbons (PAHs) are potent carcinogenic chemicals. Exposure of different fish species to PAHs causes a high prevalence and variety of tumor lesions. To identify and compare the mode of action (MOA) of different model carcinogenic PAHs, a transcriptomic study was carried out in adult zebrafish (Danio rerio) after exposure to 0.3 mg/l of benzo(a)pyrene (B(a)P) or to 7,12-dimethylbenz(a)anthracene (DMBA), both of them dissolved in dimethyl sulfoxide (DMSO; final concentration of 0.01%). Samples for microarray analysis were taken after 1 and 2 weeks of exposure. The changes in the mRNA transcription levels over the corresponding controls were compared among treatments. Correspondence analysis was able to discriminate among treatments; factor 1 separated both sampling times while factor 2 separated the compounds. A total number of 3043 transcripts was shown to be differentially regulated in at least one of the treatments. B(a)P treatment produced regulation of sequences related to GO categories associated to cell cycle and cell division whereas DMBA regulated GO terms related to oxidation/reduction responses, responses to chemicals and response to bacterium. Both compounds were able to alter many xenobiotic metabolism related genes, especially upregulating the transcription of phase I metabolism-related genes such as cytochrome P450 members (cyp1a or cyp1b), and many cancer-related genes such as the Jun B proto-oncogene (junb). Overall, these results indicated that the exposure to both PAHs was able to differentially alter the transcription levels of genes involved in both the detoxification metabolism and the cell-cycle control, including different tumor-supressor genes and oncogens. These alterations have been often related to the appearance of tumor lesions. Zebrafish were waterborne exposed to 0.3ppm BaP or DMBA for 1 and 2 weeks. After 1 and 2 weeks hepatic samples were collected from each treatment group as well as from the control group. 3 biological replicates have been collected per exposure group and time point. Each biological replicate is a pool of 5 livers. Samples from the different treatments were hybridized in an n+2 (n = 9) A-optimal loop design. Additionally, these two designs were linked by two extra hybridizations to enable comparison between time points

Project description:This study aims to evaluate the transcriptome alterations, through cDNA libraries, associated with the effects of the combination of two PAHs, benzo[a]pyrene (0.5μg/L) and phenanthrene (50μg/L), present in crude oil, on specimens of Symphysodon aequifasciatus (discus fish) after 48h of exposure. The cDNA libraries were constructed according to the SOLiDTM SAGETM protocol for sequencing in the SOLiD v.3 Plus sequencer. The results were analyzed by bioinformatics and differentially expressed genes were categorized using the gene ontology program (AmiGO v.1.8). The functional categories (terms) found in the gene ontology and the gene network generated using STRING software were used to predict the adverse effects in the liver. In the present study, 27,127 genes (compared to Danio rerio database) were identified. Considering only those genes with a p-value less than or equal to 0.05 and a greater than or equal to two-fold change in expression across libraries, we found 804 genes, 438 down-regulated (54%) and 366 up-regulated genes (46%), in the experimental group compared to the control group. Out of this total, 327 genes were successfully categorized, 174 down-regulated and 153 up-regulated genes, using gene ontology tool. The final confidence gene network, analyzed in STRING, was composed by 199 nodes of proteins, 124 of them resulted in 274 interactions. The results showed that even an acute exposure of 48 h caused metabolic change in response to environmental contaminants, resulting in changes of cell integrity, changes in oxidation-reduction processes, disturbances of intracellular signaling and changes in the immune response of discus fish. Also the gene network interactions have showed no central interplay cluster, exhibiting interconnected clusters interactions and sparsely connected sub-networks. These findings highlight that even an acute and sublethal exposure of PAHs can cause metabolism changes that may affect this fish species survival rates. Our findings using the SAGE-method and the SOLiD sequencer showed that this is a powerful tool for gene expression analysis in discus fish, a non-model organism.

Dataset Information

Functional categorization of transcriptome in the species Symphysodon aequifasciatus Pellegrin 1904 (Perciformes: Cichlidae) exposed to benzo[a]pyrene and phenanthrene

Publications

Functional categorization of transcriptome in the species Symphysodon aequifasciatus Pellegrin 1904 (Perciformes: Cichlidae) exposed to benzo[a]pyrene and phenanthrene.

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