Dissolved and particulate copper exposure induce differing gene expression profiles in a deposit feeding amphipod
Ontology highlight
ABSTRACT:
ORGANISM(S): Melita plumulosa
PROVIDER: GSE49691 | GEO | 2013/08/10
SECONDARY ACCESSION(S): PRJNA214748
REPOSITORIES: GEO
Similar Datasets
Project description:The southeastern Australian epibenthic amphipod Melita plumulosa was exposed to copper via different routes of exposure for 48 hours. RNA from exposed animals (10 individuals, pooled) was hybridised against reference RNA from unexposed animals. Each treatment was replicated 5 times. Alternate arrays were dye swapped. Data are presented (exposed/ unexposed).
2013-08-10 | E-GEOD-49691 | biostudies-arrayexpress
Project description:The southeastern Australian epibenthic amphipod Melita plumulosa was exposed to eight different contaminants for 48 hours.
2013-07-11 | GSE48658 | GEO
Project description:Chemical contamination is a common threat to biota thriving in estuarine and coastal ecosystems. In particular, trace metals tend to accumulate and exert deleterious effects on small invertebrates such as zooplankton, which are essential trophic links between phytoplankton and higher-level consumers in aquatic food webs. Beyond the direct effects of the contamination, we hypothesized that metal exposure could also affect the zooplankton microbiota, which in turn might further impair host fitness. To assess this assumption, copepods (Eurytemora affinis) were sampled in the oligo-mesohaline zone of the Seine estuary and exposed to dissolved copper (25 µg.L-1) over a 72-hour time period. Copepod response to copper treatment was assessed by determining transcriptomic changes in E. affinis along with shifts in its microbiota. Unexpectedly, very few genes were differentially expressed in copper-treated copepods compared to controls, with most of the reported differences involving genes upregulated in males compared to females. In contrast, copper increased the taxonomic diversity indices of the microbiota and resulted in substantial compositional changes at both the phyla and genus levels. Phylogenetic reconstruction of the microbiota further suggested that copper mitigated phylogenetic relatedness of taxa at the basal tree structure of the phylogeny, whereas it strengthened it at the terminal branches. Increased terminal phylogenetic clustering in copper-treated copepods concurred with higher proportions of bacterial genera previously identified as copper resistant (e.g., Pseudomonas, Acinetobacter, and Alkanindiges) and a higher relative abundance of the copA gene encoding a periplasmic inducible multi-copper oxidase. Overall, these results revealed very contrasting responses of E. affinis and its microbiota to copper exposure. The enrichment in micro-organisms likely to perform copper sequestration and/or enzymatic transformation processes, underlines here the need to follow the microbial component during the evaluation of the vulnerability of the zooplankton to the metallic stress.
2023-06-29 | GSE212602 | GEO
Project description:The southeastern Australian epibenthic amphipod Melita plumulosa was exposed to eight different contaminants for 48 hours. RNA from exposed animals (10 individuals, pooled) was hybridised against reference RNA from unexposed animals. Each treatment was replicated 5 times. Alternate arrays were dye swapped. Data are presented (exposed/unexposed).
2013-07-11 | E-GEOD-48658 | biostudies-arrayexpress
Project description:To identify genes which are differentially expressed in Corynebacterium glutamicum in the absence of copper, we performed DNA microarray analyses of cells cultivated under copper starvation conditions compared to copper sufficiency.
2018-08-28 | GSE117530 | GEO
Project description:Copper-limiting growth conditions were thought to cause an induction of genes possibly involved in copper uptake and sorting. This rationale in mind, we performed microarray analyses on B. japonicum cells grown in three variations of the BVM minimal medium. Variant 1 contained 2 μM CuSO4 (copper excess). Variant 2 was prepared in HCl-treated glassware without any copper added (copper starvation). The residual copper concentration in this copper-starvation medium was analyzed by GF-AAS and determined to be 5 nM. Variant 3 (extreme copper limitation) was prepared like variant 2 but with the addition of 10 μM BCS and 1 mM ascorbic acid where BCS chelates Cu(I) selectively, and ascorbic acid reduces any Cu(II) to Cu(I). Changes in the transcription profiles were recorded by the pairwise comparison of cells grown in variant 2 vs. 1, and variant 3 vs. 2. Only a small set of genes were differentially up- or down-regulated when copper-starved cells were compared with cells grown in copper excess. Most notably, five genes located adjacent to each other on the B. japonicum genome displayed an increased expression: bll4882 to bll4878. The five genes were named pcuA, pcuB, pcuC, pcuD, and pcuE (mnemonic of proteins for Cu trafficking). The genes with decreased expression are either of unknown function or – not surprisingly – play a role in copper resistance. Extreme copper limitation (variant 3 vs. 2) did not further enhance the expression of the five pcu genes. Instead, another cluster of adjacent genes was strongly up-regulated: bll0889 to bll0883, which code for unidentified transport functions. Incidentally, the list also includes the copper chaperone ScoI. Taken together, copper-limiting growth conditions have led to the de-repression of genes potentially involved in copper acquisition.
2012-10-01 | GSE40437 | GEO
Project description:Copper and iron are essential micronutrients for most living organisms because they participate as cofactors in biological processes including respiration, photosynthesis and oxidative stress protection. In many eukaryotic organisms, including yeast and mammals, copper and iron homeostases are highly interconnected; however such interdependence is not well established in higher plants. Here we propose that COPT2, a high-affinity copper transport protein, functions under copper and iron deficiencies in Arabidopsis thaliana. COPT2 is a plasma membrane protein that functions in copper acquisition and distribution. Characterization of the COPT2 expression pattern indicates a synergic response to copper and iron limitation in roots. We have characterized a knockout of COPT2, copt2-1, that leads to increased resistance to simultaneous copper and iron deficiencies, measured as reduced leaf chlorosis and improved maintenance of the photosynthetic apparatus. We propose that COPT2 expression could play a dual role under Fe deficiency. First, COPT2 participates in the attenuation of copper deficiency responses driven by iron limitation maybe aimed to minimize further iron consume. On the other hand, global expression analyses of copt2-1 mutants versus wild type Arabidopsis plants indicate that low phosphate responses are increased in copt2-1 plants. In this sense, COPT2 function under Fe deficiency counteracts low phosphate responses. These results open up new biotechnological approaches to fight iron deficiency in crops.
2013-06-05 | GSE42642 | GEO
Project description:Copper-limiting growth conditions were thought to cause an induction of genes possibly involved in copper uptake and sorting. This rationale in mind, we performed microarray analyses on B. japonicum cells grown in three variations of the BVM minimal medium. Variant 1 contained 2 M-NM-<M CuSO4 (copper excess). Variant 2 was prepared in HCl-treated glassware without any copper added (copper starvation). The residual copper concentration in this copper-starvation medium was analyzed by GF-AAS and determined to be 5 nM. Variant 3 (extreme copper limitation) was prepared like variant 2 but with the addition of 10 M-NM-<M BCS and 1 mM ascorbic acid where BCS chelates Cu(I) selectively, and ascorbic acid reduces any Cu(II) to Cu(I). Changes in the transcription profiles were recorded by the pairwise comparison of cells grown in variant 2 vs. 1, and variant 3 vs. 2. Only a small set of genes were differentially up- or down-regulated when copper-starved cells were compared with cells grown in copper excess. Most notably, five genes located adjacent to each other on the B. japonicum genome displayed an increased expression: bll4882 to bll4878. The five genes were named pcuA, pcuB, pcuC, pcuD, and pcuE (mnemonic of proteins for Cu trafficking). The genes with decreased expression are either of unknown function or M-bM-^@M-^S not surprisingly M-bM-^@M-^S play a role in copper resistance. Extreme copper limitation (variant 3 vs. 2) did not further enhance the expression of the five pcu genes. Instead, another cluster of adjacent genes was strongly up-regulated: bll0889 to bll0883, which code for unidentified transport functions. Incidentally, the list also includes the copper chaperone ScoI. Taken together, copper-limiting growth conditions have led to the de-repression of genes potentially involved in copper acquisition. Microarray-based transcriptome analysis of B. japonicum 110spc4 wild-type cells grown under normal, copper-limiting and copper excess conditions
2012-10-01 | E-GEOD-40437 | biostudies-arrayexpress
Project description:Analysis of genome-wide gene expression patterns in response to copper in WT and COPR mutant in the cyanobacterium Synechocystis sp PCC 6803. Here we have used microarrays to interrogate the global responses to copper additions at non-toxic (0.3 micromolar) and toxic concentrations (3 micromolar) of copper in WT and in a mutant in the copR gene. Addition of the non-toxic copper concentration stimulated the metabolism and induced the switch in the use from cyitochrome c6 to plastocyanin. In contrast, high copper addition induced a stress response and affected the metabolism of several other metals. This included repression of ribosomal, photosynthetic and metabolic genes and induction of chaperones and antioxidant enzymes genes. Finally CopRS seems to control only the expression of the copMRS and copBAC operons as all other genes that were differentially expressed by copper seemed to be unaffected in copR strains.
2014-09-01 | GSE51671 | GEO