Molecular mechanisms of zinc toxicity in the potworm Enchytraeus crypticus, analysed by high-throughput gene expression profiling
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ABSTRACT:
ORGANISM(S): Enchytraeus crypticus
PROVIDER: GSE183377 | GEO | 2022/02/21
REPOSITORIES: GEO
Similar Datasets
Project description:The soil worm Enchytraeus crypticus (oligochaete) is an ecotoxicology model species although without genome or transcriptome sequence information. The present research aimed at studying, via high-throughput pyrosequencing, the transcriptome of Enchytraeus crypticus, sampled from multiple test conditions, and the construction of a high-density microarray for functional genomic studies. A pyrosequencing run retrieved approximately 1.5 million reads representing 645 million bases. After assembly, 27,296 contigs and 87,686 singletons were obtained. from which 44% and 25% were annotated as protein-coding genes. We show that the high amount of orphan genes is not due to poor sequence or assemble quality: 84% of the contig sequences contains an open reading frame with a start codon and E. crypticus homologs were identified for 92% of the core eukaryotic genes. Moreover, 65 and 77% of the unknown singletons and contigs, respectively, showed transcriptional activity. An Agilent 180K microarray platform was designed and validated by hybridizing cDNA from 3 day zinc- exposed E. crypticus to the concentration corresponding to 50% reduction in reproduction (EC50). Overall, 70% of all probes exerted a hybridization signal above background level. More specifically, the probes derived from contigs showed a wider range of average intensities when compared to probes derived from singletons. In total, 522 significantly regulated transcripts were identifying upon zinc exposure. Several significantly regulated genes exerted predicted functions (e.g. zinc efflux, zinc transport) associated with zinc stress. Unexpectedly, the microarray data suggest that zinc exposure alters retrotransposon activity in the E. crypticus genome. In conclusion, characterization of the presented E. crypticus transcriptome and associated microarray platform is a valuable and high quality resource that permits further functional genomics experiments examining gene expression patterns underlying distinct environmental stress conditions. We show that unknown sequences are not the result of technical errors but mostly represent functional genes that are actively transcribed. The data presented in our manuscript is part of a larger experiment which was performed in single, large loop design. The analysis presented here can be replicated only by including all raw data from the larger experiment (all raw files are included in the archive linked to this submission). A single channel, interwoven loop design was used to test animals exposed to zinc EC50 on reproduction as compared to untreated controls for 4 days. 4 biological replicates per condition were used containing 25 grams of soil and 5 - 7, adult old animals per replicate. T4_con stands for untreated control soil while T4_50 are the samples exposed to EC50 of zinc on reproduction.
2014-05-01 | E-GEOD-51838 | biostudies-arrayexpress
Project description:Understanding the mode of action of nanomaterials (NMs) aids in improving predictions and environmental risk assessment. In the present study, a high-throughput (HTP) microarray was used to study Enchytraeus crypticus gene expression. Four Ag materials (Ag NM300K, PVP-coated AgNPs, AgNPs, and AgNO3) were tested at reproduction effect concentrations, EC20 and EC50, to anchor gene expression responses to higher effect level. The results showed that while PVP-AgNPs and AgNPs had similar responses, Ag NM300K caused effects via a differentiated transcriptomic profile, with uniquely affected processes (e.g. transcytosis). For the AgNPs, the EC50 negatively affected apoptosis, which can lead to accumulation of abnormal cells and cause apical damage (reproduction). Mechanisms which are known to be related to Ag toxicity and which were observed here for the various Ag forms included apoptosis regulation, cell redox homeostasis, impairment of energy production and response to DNA damage. This HTP genomic tool enabled discrimination between Ag materials, which is not possible via standard tests (i.e. survival and reproduction endpoints). Moreover, gene expression analysis provided information regarding the mechanisms of toxicity of NMs and the pathways uniquely affected by NMs. An adverse outcome pathway (AOP) was drafted for the first time for Ag NMs; this AOP can and should be used as a basis for further research.
2017-03-24 | GSE69746 | GEO
Project description:Metal ecotoxicity on soil organisms, e.g. in Enchytraeids (also known as potworms), has been addressed mainly by assessing effects on survival and reproduction but very little is known about the molecular underlying mechanisms of responses. The main purpose of the present study was to assess and compare the transcriptional responses of Enchytraeus albidus to an essential (zinc) and a non-essential metal (cadmium). Exposure was performed to two concentrations of known effect on reproduction (EC50, EC90) at three time periods (2, 4 and 8 days). Results showed that transcriptional responses were influenced by exposure duration but, independently of that, the mechanisms of response to Cd and Zn were consistently different. Both metals affected pathways related with the regulation of gene expression, calcium homeostasis and cellular respiration. Mechanisms of toxicity that were exclusively associated with Cd exposures were the inhibition of DNA repair and the impairment of ubiquitin-mediated proteolysis. The microarray for E. albidus was a useful tool to detect molecular pathways affected by metal exposures. Transcriptional responses strongly correlated with known mechanisms of Cd and Zn responses in other organisms, suggesting cross-species conserved mechanisms of action. It should be highlighted that we could not only retrieve mechanistic information, but also that genes responded within 2-8 days of exposure. This represents an additional advantage of using such molecular endpoints as a complement to the traditional, more time-consuming endpoints. Gene expression in E.albidus was measured at 2, 4, and 8 days after exposure to Cadmium and Zinc at 2 concentrations of effect on reprocduction (EC50 and EC90). Three biological replicates per exposure treatment in each time point and 4 biological replicates of control conditions were used.
2012-06-30 | E-GEOD-33944 | biostudies-arrayexpress
Project description:The soil worm Enchytraeus crypticus (oligochaete) is an ecotoxicology model species although without genome or transcriptome sequence information. The present research aimed at studying, via high-throughput pyrosequencing, the transcriptome of Enchytraeus crypticus, sampled from multiple test conditions, and the construction of a high-density microarray for functional genomic studies. A pyrosequencing run retrieved approximately 1.5 million reads representing 645 million bases. After assembly, 27,296 contigs and 87,686 singletons were obtained. from which 44% and 25% were annotated as protein-coding genes. We show that the high amount of orphan genes is not due to poor sequence or assemble quality: 84% of the contig sequences contains an open reading frame with a start codon and E. crypticus homologs were identified for 92% of the core eukaryotic genes. Moreover, 65 and 77% of the unknown singletons and contigs, respectively, showed transcriptional activity. An Agilent 180K microarray platform was designed and validated by hybridizing cDNA from 3 day zinc- exposed E. crypticus to the concentration corresponding to 50% reduction in reproduction (EC50). Overall, 70% of all probes exerted a hybridization signal above background level. More specifically, the probes derived from contigs showed a wider range of average intensities when compared to probes derived from singletons. In total, 522 significantly regulated transcripts were identifying upon zinc exposure. Several significantly regulated genes exerted predicted functions (e.g. zinc efflux, zinc transport) associated with zinc stress. Unexpectedly, the microarray data suggest that zinc exposure alters retrotransposon activity in the E. crypticus genome. In conclusion, characterization of the presented E. crypticus transcriptome and associated microarray platform is a valuable and high quality resource that permits further functional genomics experiments examining gene expression patterns underlying distinct environmental stress conditions. We show that unknown sequences are not the result of technical errors but mostly represent functional genes that are actively transcribed.
2014-05-01 | GSE51838 | GEO
Project description:Metals, including copper (Cu) and nickel (Ni) are among the most common contaminants in soils in Europe. Although their effects are relatively well known regarding survival and reproduction of soil invertebrates, their modes of action in these organisms are still poorly studied. Enchytraeus albidus has been used in soil ecotoxicology for many years, and more recently has a gene library and an oligonucleotide microarray for this species which allowed gene expression studies. This has potentiated the means to study further in depth the mechanisms of response to stressors. The main aim of this study is to understand the mechanisms of response of E. albidus to Cu and Ni. For that we have 1) assessed and compared the transcriptomic profile of E. albidus in response to Cu and Ni and 2) compared the Cu, Ni, Cd and Zn transcriptomic profiles. For the microarray hybridizations, E. albidus were exposed to the reproduction effect concentrations EC50 and EC90 of Cu and Ni during 4 days. Results indicate that Cu and Ni have to some extent, similar mechanisms of toxicity and that have already been identified in other species, indicating cross-species conserved mechanisms. Based on hierarchical clustering, it was possible to observe a clear separation of Cd treatments from all other metals. This separation strongly correlates with the available information regarding the toxicokinetics of the tested metals, in which Ni shows properties similar to essential metals. Gene expression in E.albidus was measured 4 days after exposure to Copper, Nickel, Cadmium and Zinc at 2 concentrations of effect on reprocduction (EC50 and EC90). Three biological replicates per exposure condition and 6 biological replicates of control conditions were used.
2013-12-31 | E-GEOD-47662 | biostudies-arrayexpress
Project description:Silver nanomaterials (AgNMs) are broadly used in many products and also rate among the most studied nanoscaled materials. Their ecotoxicological impact in soil invertebrates has been covered, mostly using standard testing, where endpoints like survival and reproduction are assessed. The underlying molecular mechanisms have been assessed to a much less extent. Hence, we here assessed differentially expressed proteins (DEPs) and metabolites (DEMs) by high-throughput (HTP) techniques (HPLC-MS/MS with tandem mass tags for proteome analysis, as well as reversed-phase (RP)- or hydrophilic interaction liquid chromatography (HILIC) with mass spectrometric detection for metabolome analysis. The standard soil model Enchytraeus crypticus was exposed to Ag NM300K and soluble AgNO3, at the reproduction EC20 and EC50, in a time series of 0, 7, and 14 days. The impact was clearly larger after 14 days. Ag NM300K caused more upregulated DEPs/DEMs, and more so at the EC20, compared to the EC50, whereas AgNO3 caused a dose response increase of DEPs/DEMs. Similar pathways were activated, although often via opposite regulation (up vs down) of DEPs hence dissimilar mechanisms underlie the apical impact. Affected pathways include e.g. energy metabolism transport proteins, detoxifying enzymes, histidine (e.g. neurotransmission by gamma-aminobutyric acid (GABA)) and lipid metabolism. Uniquely affected by AgNO3 were catalase, malate dehydrogenase and ATP-citrate synthase, and by Ag NM300K were heat shock proteins (HSP70) and ferritin. The gene expression-based data in Adverse Outcome Pathway (AOP) was confirmed and additional key events were added. Evidences support that toxicity of Ag NM increases in longer-term exposure.
2021-09-10 | PXD024444 | Pride
Project description:Polycyclic Aromatic Hydrocarbons (PAHs) continue to cause environmental challenges due to their release in the environment by a great variety of anthropogenic activities and their accumulation in soil ecosystems. Here we studied the toxicological effect of the model PAH phenanthrene (Phe) on the soil invertebrate model Enchytraeus crypticus at the individual, tissue and molecular level. Organisms were exposed to Phe for 2 and 21 days to the (previously estimated) EC10 and EC50 (population reproduction over 3 weeks). Gene expression profiling did not reveal a typical Phe-induced biotransfor-mation signature, as it usually does in arthropods and vertebrates. Instead, we observed only general metabolic processes to be affected after 2 days of exposure, such as translation and ATP synthesis-coupled electron transport. Histological sections of tissues of 2-day exposed animals did not show any deviations from the control situation. In contrast, prolonged exposure up to 21 days showed histopathological effects: chloragogenous cells were highly vacuolated and hypertrophic. This was corroborated by differential expression of genes related to immune response and oxidative stress at the transcriptomic level. The data exemplify the complexity and species-specific features of PAH toxicity among soil invertebrate communities, which restricts read-across and extrapolation in the context of soil ecological risk assessment. The data presented in our manuscript is an exposure experiment where E. cryticus is exposed to phenanthrene EC10 and EC50 on reproduction for 2 and 21 days. A single channel, interwoven loop design was used to test animals. 4 biological replicates per condition were used containing 25 grams of soil and 5 - 7, adult old animals per replicate. The platform is a 4*180k Agilent platform containing some 86k E. crypticus probes in duplicate. However, only a subset of the probes (23k) was used for the analysis. To see which probes were used in the analysis see the raw data files control type column, only probes which are denoted with a 0 were used.
2015-12-18 | E-GEOD-74114 | biostudies-arrayexpress
Project description:Metal ecotoxicity on soil organisms, e.g. in Enchytraeids (also known as potworms), has been addressed mainly by assessing effects on survival and reproduction but very little is known about the molecular underlying mechanisms of responses. The main purpose of the present study was to assess and compare the transcriptional responses of Enchytraeus albidus to an essential (zinc) and a non-essential metal (cadmium). Exposure was performed to two concentrations of known effect on reproduction (EC50, EC90) at three time periods (2, 4 and 8 days). Results showed that transcriptional responses were influenced by exposure duration but, independently of that, the mechanisms of response to Cd and Zn were consistently different. Both metals affected pathways related with the regulation of gene expression, calcium homeostasis and cellular respiration. Mechanisms of toxicity that were exclusively associated with Cd exposures were the inhibition of DNA repair and the impairment of ubiquitin-mediated proteolysis. The microarray for E. albidus was a useful tool to detect molecular pathways affected by metal exposures. Transcriptional responses strongly correlated with known mechanisms of Cd and Zn responses in other organisms, suggesting cross-species conserved mechanisms of action. It should be highlighted that we could not only retrieve mechanistic information, but also that genes responded within 2-8 days of exposure. This represents an additional advantage of using such molecular endpoints as a complement to the traditional, more time-consuming endpoints.
2012-07-01 | GSE33944 | GEO
Project description:The testing of NMs under the currently available standard toxicity tests does not cover many of the NMs specificities. One of the current recommended approaches forward lays on understanding the mechanisms of action as these can help predicting long term effects and safe-by-design production. Copper nanomaterials (Cu-NMs) usage has been highly increasing with the concern in terms of exposure, effect and associated risks. In the present study we used the high-throughput gene expression tool developed for Enchytraeus crypticus (44Kx4 Agilent microarray) to study to the effect of exposure to several copper forms. The copper treatments include two NMs (spherical and wires) and two copper-salt treatments (CuNO3 spiked and Cu field historical contamination). Testing was done based on reproduction effect concentrations (EC20, EC50) using 3 and 7 days exposure periods.
2017-06-13 | GSE69792 | GEO
Project description:The effect of nanomaterials (NMs) is less understood in light of the implemented and existing methodologies for regular chemicals. To understand the mode of action of NMs is one of the alternatives to improve predictions and environmental risk assessment (ERA). In the present work the high-throughput gene expression tool (4x44K microarray for Enchytraeus crypticus) was used to investigate the mechanisms activated by Ni exposure. Ni nanoparticles (Ni-NPs) were investigated together with Ni-salt (NiNO3). Testing was done based on reproduction effect concentrations (EC20, EC50) using 3 and 7 days exposure periods.
2017-06-13 | GSE69793 | GEO