Transcriptomic profiles reveal the genome-wide responses of the harmful dinoflagellate Cochlodinium polykrikoides (Cp) when exposed to the algicide copper sulfate
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ABSTRACT:
ORGANISM(S): Margalefidinium polykrikoides
PROVIDER: GSE75463 | GEO | 2017/02/10
REPOSITORIES: GEO
Similar Datasets
Project description:The effect of the heavy metal copper on the expression of a wide spectrum of genes was analyzed by using a DNA microarray. Gene expression profile of baker’s yeast Saccharomyces cerevisiae grown in a media containing sub-lethal concentration of cupric sulfate was compared with those of yeast grown in a normal media. Among about 6200 ORFs of yeast, 143 ORFs were induced more than two-fold to resist against copper toxicity after exposure to copper. As was expected, FRE1, FRE7, and CTR1, genes controlled by Mac1p, were strongly down-regulated. Copper metallothionein CUP1-1 and CUP1-2 were induced more than 20-fold. Some genes related to sulfur metabolism and oxidative stress response were also up-regulated. This DNA microarray technology indicated that plasma membrane, cell wall, protein, and DNA, were molecular targets of copper toxicity. Keywords: stress response
2007-11-01 | GSE9231 | GEO
Project description:Each strain was grown overnight then diluted in fresh rich media. After three hours strains were again rediluted into either rich media or rich media supplemented with copper sulfate. After another three hours cultures were sampled, cells lysed and flash frozen using liquid nitrogen. RNA was extrated using hot phenol-chloroform, reverse transcripbed using amino-allyle dUTP and labelled with either Cy3 or Cy5 flourescent dye. Each hybridization is of a single sample compared to a reference pool contructed from all the strains with the same treatment. Labelled probe were hybridized to DNA microarrays spotted with 6144 70 bp oligonucleotides obtained from Qiagen-Operon. After an overnight hybridization, microarrays were scanned using a GenePix 4000A scanner and spot intensities extracted using GenePix 4.0 software. Bad spots were flagged based on the image. Keywords: other
2004-03-01 | GSE1073 | GEO
Project description:MAP kinases are integral to the mechanisms by which cells respond to a wide variety of environmental stresses. In Caenorhabditis elegans, the KGB-1 JNK signaling pathway regulates the response to heavy metal stress. The deletion mutants of this cascade show hypersensitivity to heavy metals like copper or cadmium. However, factors that function downstream of KGB-1 pathway are not well characterized. To understand how the KGB-1 pathway modulates gene activity and to define the physiological processes in which the heavy metal stress response may be involved, we used microarray to examine gene expression changes in wild-type and kgb-1 mutant animals subjected to heavy metal stress. Adult worms of WT or kgb-1 mutant were incubated with H2O or 1 mM copper sulfate for 1 hour. Total RNA was then prepared using Trizol reagent (Invitrogen), followed by DNase I treatment, phenol/chloroform extraction and ethanol precipitation. (WT_Cu-), (WT_Cu+), (kgb-1_Cu-) and (kgb-1_Cu+) RNAs extraction were hybridized on Affymetrix microarrays.
2012-12-05 | E-GEOD-42703 | biostudies-arrayexpress
Project description:In this study, we report the identification of a five-locus copper-inducible regulon in Mycobacterium tuberculosis. The identification of a copper responsive regulon unique to pathogenic Mycobacteria suggests copper homeostasis must be maintained during an infection. WT and mutant Mtb cells were grown in Sauton's minimal media to early stationary phase (OD580 = 1.5) and treated with 500 mM copper sulfate (CuSO4) for four hours or the absence
2010-10-27 | E-GEOD-23498 | biostudies-arrayexpress
Project description:The expression profile of natural isolate of S. cerevisiae carrying different copy of CUP2 were compared under cooper sulfate stress The gene expression profiles of natural isolate of S.cerevisiae(EC9-7), EC9-7 cup2∆ and Ec9-7 cup2∆cup2∆ strains under YPD with 1mM copper sulfate for 1h and rich medium(YPD) were compared.
2011-08-25 | E-GEOD-31661 | biostudies-arrayexpress
Project description:Harmful algal blooms (HABs) caused by the dinoflagellate Cochlodinium polykrikoides lead to severe environmental impacts in oceans worldwide followed by huge economic losses. Algicide agent copper sulfate (CuSO4) is regard as an economical and effective agent for HABs mitigation; its biochemical and physiological effects were revealed in C. polykrikoides. However, molecular mechanisms of CuSO4 effect on the C. polykrikoides, even other HAB species, have not been investigated. The present study investigated the transcriptional response of C. polykrikoides against CuSO4 treatments, with the aim of providing certain molecular mechanism of CuSO4 effect on the C. polykrikoides blooms.RNA-seq generated 173 million reads, which were further assembled to 191,212 contigs. 43.3 %, 33.9 %, and 15.6 % of contigs were annotated with NCBI NR, GO, and KEGG database, respectively. Transcriptomic analysis revealed 20.6 % differential expressed contigs, which grouped into 8 clusters according to K-means clustering analysis, responding to CuSO4; 848 contigs were up-regulated and 746 contigs were down-regulated more than 2-fold changes from 12 h to 48 h exposure. KEGG pathway analysis of eukaryotic homologous genes revealed the differentially expressed genes (DEGs) were involved in diverse pathway; amongst, the genes involved in the translation, spliceosome, and/or signal transduction genes were highly regulated. Most of photosystem related genes were down-regulated and most of mitochondria related genes were up-regulated. In addition, the genes involved in the copper ion binding or transporting and antioxidant systems were identified. Measurement of chlorophyll fluorescence showed that photosynthesis was significantly inhibited by CuSO4 exposure.This study reported the first transcriptome of the C. polykrikoides. The widely differential expressed photosystem genes suggested photosynthetic machinery were severely affected, and may further contribute to the cell death. Furthermore, gene translation and transcription processes may be disrupted, inhibiting cell growth and proliferation, and possibly accelerating cell death. However, antioxidant systems resistant to CuSO4 caused stress; mitochondrion may compensate for photosynthesis efficiency decreasing caused energy deficiency. In addition, various signal transduction pathways may be involved in the CuSO4 induced regulation network in the C. polykrikoides. These data provide the potential transcriptomic mechanism to explain the algicide CuSO4 effect on the harmful dinoflagellate C. polykrikoides.
| S-EPMC4702327 | biostudies-literature
Project description:dinoflagellate metagenome Metagenome
| PRJNA503759 | ENA
Project description:In this study, we report the identification of a five-locus copper-inducible regulon in Mycobacterium tuberculosis. The identification of a copper responsive regulon unique to pathogenic Mycobacteria suggests copper homeostasis must be maintained during an infection. WT and mutant Mtb cells were grown in Sauton’s minimal media to early stationary phase (OD580 = 1.5) and treated with 500 mM copper sulfate (CuSO4) for four hours or the absence.
2011-11-01 | E-GEOD-24968 | biostudies-arrayexpress
Project description:Copper tolerance and sulfite tolerance are two well-studied phenotypic traits of Saccharomyces cerevisiae. The genetic bases of these traits are derived from allelic expansion at the CUP1 locus and reciprocal translocation at the SSU1 locus, respectively. Previous work identified a negative association between sulfite and copper tolerance in S. cerevisiae wine yeasts. Here we probe the relationship between sulfite and copper tolerance and show that an increase in CUP1 copy number does not impart copper tolerance in all S. cerevisiae wine yeast. Bulk-segregant QTL analysis was used to identify variance at SSU1 as a causative factor in copper sensitivity, which was verified by reciprocal hemizygosity analysis in a strain carrying 20 copies of CUP1. Transcriptional and proteomic analysis demonstrated that SSU1 over-expression did not suppress CUP1 transcription or constrain protein production but suggested that SSU1 overexpression induced sulfur limitation during exposure to copper. Finally, an SSU1 over-expressing strain exhibited increased sensitivity to moderately elevated copper concentrations in sulfur-limited medium, demonstrating that SSU1 over-expression burdens the sulfate assimilation pathway. Over-expression of MET 3/14/16, genes upstream of H2S production in the sulfate assimilation pathway increased the production of SO2 and H2S but did not improve copper sensitivity in an SSU1 overexpressing background. We conclude that copper and sulfite tolerance are conditional traits in S. cerevisiae and provide evidence of the metabolic basis for their mutual exclusivity. These findings suggest an evolutionary basis for the extreme amplification of CUP1 observed in some yeasts.
2023-03-22 | PXD037997 | Pride
Project description:Dynamic transcriptional response of S. cerevisiae cells to copper impulse was investigated in both HO deletion strain used as the reference strain and the mutant strain lacking CCC2 gene which were grown in continuous cultures using a copper-deficient defined medium. Copper was introduced into the medium as an impulse so as to reach a copper sulfate concentration of 0.5 mM. Samples were collected within the first two hours following the copper addition (1st, 5th, 10th, 15th, 20th, 25th, 30th, 60th, 120th minutes), in addition to the steady-state sampling.
2020-10-28 | E-MTAB-9155 | biostudies-arrayexpress