Effects of zinc ions and HrasG12V-activated signaling on gene expression of rat embryonic fibroblasts maintained in serum-free media
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA756373 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To identify intracellular events affected by HrasG12V and zinc ion availability, gene expression profiling was performed with Rat-1·RasValA1, a stably transfected cell line where oncogenic mutant HrasG12V is expressed under the control of an IPTG-inducible promoter. Rat-1·RasValA1 cells were treated for 24 h with or without 5 mM IPTG in serum-free DMEM in the presence or absence of ZnCl2 supplementation at 3 microM. Total RNA was purified for gene expression profiling with microarray.
2022-02-27 | GSE182481 | GEO
Project description:The toxicity of silver and zinc oxide nanoparticles is hypothesised to be mediated by dissolved metal ions and cerium dioxide nanoparticles (CeO2 NPs) are hypothesised to induce toxicity specifically by oxidative stress dependant on their surface redox state. To test these hypotheses, RNAseq was applied to characterise the molecular responses of cells to metal nanoparticle and metal ion exposures. The human epithelial lung carcinoma cell line A549 was exposed to different CeO2 NPs with different surface charges, micron-sized and nano-sized silver particles and silver ions, micron-sized and nano-sized zinc oxide particles and zinc ions, or control conditions, for 1 hour, 6 hours and 24 hours. Concentrations were the lower of either EC20 or 128 micrograms/mL. Transcriptional responses were characterised by RNAseq transcriptomics using an Illumina HiSeq2500 .
2018-02-01 | E-MTAB-5734 | biostudies-arrayexpress
Project description:Salmonella can infect a wide range of hosts and survive in the environment. This invasive pathogen has therefore evolved and acquired specific traits to cope with different, and in most cases unfavorable, conditions. In particular, transition metal ions are widely spread in these niches. These ions are essential in biology and play key roles in the structure-function of a large number of proteins. They can also be toxic, especially at high concentrations. Intracellular metal ion concentrations must therefore be tightly controlled to maintain normal metabolism. Salmonella has acquired traits to deal with the presence of toxic concentrations of some of these ions and, at the same time, to fulfill its requirement for essential metal ions when they are scarce. In this work we analyze the transcriptional response of Salmonella enterica to copper and zinc, two of these essential metals, in both rich (SLB) and defined (M9) media and at short times (10 minutes). This tiling-array based work provides a detailed description of the main transcriptional response when Salmonella detects fluctuations in copper and zinc concentrations.
2012-03-15 | GSE35328 | GEO
Project description:Zinc is a central player in the metalloproteomes of prokaryotes and eukaryotes. We used a top-down quantitative proteomic approach to reveal the repository of the zinc pools in the proteobacterium Cupriavidus metallidurans. About 60% of the theoretical proteome of C. metallidurans were identified, quantified, and compared between a ΔzupT mutant defect in zinc allocation and its parent strain. In both strains, the number of zinc-binding proteins and their binding sites exceeded that of the zinc ions per cell, indicating that the totality of the zinc proteome provides empty binding sites for incoming zinc ions. This zinc repository plays a central role in zinc homeostasis in C. metallidurans and probably also in other organisms.
2016-05-04 | PXD001356 | Pride
Project description:eIF2B5 is necessary for HrasG12V hyperplastic growth. Ribosome profiling was used to describe HrasG12V and WT dependence on eIF2B5-mediated translation.
2020-06-10 | GSE126660 | GEO
Project description:Salmonella can infect a wide range of hosts and survive in the environment. This invasive pathogen has therefore evolved and acquired specific traits to cope with different, and in most cases unfavorable, conditions. In particular, transition metal ions are widely spread in these niches. These ions are essential in biology and play key roles in the structure-function of a large number of proteins. They can also be toxic, especially at high concentrations. Intracellular metal ion concentrations must therefore be tightly controlled to maintain normal metabolism. Salmonella has acquired traits to deal with the presence of toxic concentrations of some of these ions and, at the same time, to fulfill its requirement for essential metal ions when they are scarce. In this work we analyze the transcriptional response of Salmonella enterica to copper and zinc, two of these essential metals, in both rich (SLB) and defined (M9) media and at short times (10 minutes). This tiling-array based work provides a detailed description of the main transcriptional response when Salmonella detects fluctuations in copper and zinc concentrations. 14028s cells were grown up to OD 0.6, then, copper 10 uM (M9) or 1 mM (SLB) or Zn 50uM (M9) or 0.25 mM (SLB) was added and bacteria were grown for 10 minutes, RNA was isolated after this time. The RNA from bacteria grown without metal was also isolated. Each sample was analized by duplicate.
2012-03-15 | E-GEOD-35328 | biostudies-arrayexpress
Project description:An antivirulence approach targets bacterial virulence rather than cell viability in the antibiotic approach that can readily lead to drug resistance. Opportunistic human pathogen Pseudomonas aeruginosa produces a variety of virulence factors, and biofilm cells of this bacterium are much more resistant to antibiotics than planktonic cells. To identify novel inorganic antivirulence compounds, the dual screenings of thirty-six metal ions were performed to identify that zinc ions and ZnO nanoparticle inhibited the pyocyanin production and biofilm formation in P. aeruginosa without affecting the growth of planktonic cells. Moreover, zinc ion and ZnO nanoparticle markedly reduced the production of 2-heptyl-3-hydroxy-4(1H)-quinolone and siderophore pyochelin, while increased the production of another sideropore pyoverdine and swarming motility. Further, zinc ion and ZnO nanoparticle clearly suppressed hemolytic activity in P. aeruginosa. Transcriptome analyses showed that ZnO nanoparticle induced zinc cation efflux pump czc operon, porin genes (oprD and opdT), and Pseudomonas type III repressor A ptrA, while repressed pyocyanin-related phz operon, which partially explains the phenotypic changes. Overall, ZnO nanoparticle is a potential candidate for use in an antivirulence approach against persistent P. aeruginosa infection.
2015-05-25 | GSE46947 | GEO
Project description:To identify the molecular pathways that are perturbed due to transient zinc chelation Zinc is known to regulate the functions of about 10% of the human proteome and a large number of physiological processes that are zinc dependent have been identified and characterized under conditions of zinc deficiency and supplementation. As zinc homeostasis is closely linked to the normal functioning of both prokaryotic and eukaryotic cells, many pathogens are directly or indirectly affected by perturbations in zinc homeostasis. Dengue virus (DENV), a mosquito-borne, positive-strand RNA virus from the family Flaviviridae, has emerged as one of the major public health concerns in India and recent estimates suggest that over 60 million people globally get infected with DENV every year. The crystal structures of NS5 protein of DENV and West Nile virus have identified zinc binding site in RdRp domain and propose an important structural role for zinc ions in polymerase activity. Therefore, we investigated whether perturbation in intracellular zinc pools influence dengue infection. We utilized N,N,N’,N’-tetrakis(2-pyridinylmethyl)-1,2-ethanediamine (TPEN), a zinc-specific chelator, to mimic zinc-deficiency in cell culture models of infection and investigated the effect of zinc depletion on DENV life-cycle.
2019-10-29 | GSE135873 | GEO
Project description:To investigate how pleiotropic the impact of p53 loss is on cellular function, generated isogenic, polyclonal wild-type (sgNTC) and p53-null (sgp53) E1A;HrasG12V mouse embryonic fibroblast cell lines using CRISPR/Cas9. Here we show gene expression analysis on p53 wild-type (sgNTC) and p53null (sgp53) E1A;HrasG12V MEFs grown under physiological oxygen conditions (5% oxygen).
2020-08-07 | GSE136355 | GEO
Project description:An antivirulence approach targets bacterial virulence rather than cell viability in the antibiotic approach that can readily lead to drug resistance. Opportunistic human pathogen Pseudomonas aeruginosa produces a variety of virulence factors, and biofilm cells of this bacterium are much more resistant to antibiotics than planktonic cells. To identify novel inorganic antivirulence compounds, the dual screenings of thirty-six metal ions were performed to identify that zinc ions and ZnO nanoparticle inhibited the pyocyanin production and biofilm formation in P. aeruginosa without affecting the growth of planktonic cells. Moreover, zinc ion and ZnO nanoparticle markedly reduced the production of 2-heptyl-3-hydroxy-4(1H)-quinolone and siderophore pyochelin, while increased the production of another sideropore pyoverdine and swarming motility. Further, zinc ion and ZnO nanoparticle clearly suppressed hemolytic activity in P. aeruginosa. Transcriptome analyses showed that ZnO nanoparticle induced zinc cation efflux pump czc operon, porin genes (oprD and opdT), and Pseudomonas type III repressor A ptrA, while repressed pyocyanin-related phz operon, which partially explains the phenotypic changes. Overall, ZnO nanoparticle is a potential candidate for use in an antivirulence approach against persistent P. aeruginosa infection. P. aeruginosa Genechip Genome Array (Affymetrix, P/N 900339) was used in order to study the cells after the addition of ZnO nanoparticles. DNA microarray analysis with one biological replicate was performed with an Affymetrix system. P. aeruginosa was inoculated in 25 ml of LB medium in 250 ml shaker flasks with overnight cultures (1 : 100 dilution). Cells were cultured for 5 h with shaking at 250 rpm with and without ZnO nanoparticles (1 mM). Before sample collection, RNase inhibitor (RNAlater, Ambion, TX, USA) was added, and the cells were immediately chilled with dry ice and 95% ethanol (to prevent RNA degradation) for 30 s before centrifugation at 16,000 g for 2 min. The cell pellets were immediately frozen with dry ice and stored at –80°C. Total RNA was isolated using a Qiagen RNeasy mini Kit (Valencia, CA, USA).
2015-05-25 | E-GEOD-46947 | biostudies-arrayexpress