Gallic acid modulates copper and iron homeostasis and antioxidant systems in Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2500
ORGANISM(S): Saccharomyces cerevisiae S288C
SUBMITTER: Todsapol Techo
PROVIDER: E-MTAB-17319 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Gallic acid modulates copper and iron homeostasis and antioxidant systems in Saccharomyces cerevisiae
| PRJEB121218 | ENA
Project description:Purpose: CsoR, a copper responsive negative regulator of Mycobacterium tuberculosis has been shown to respond to copper and bind to its own regulon in in vitro experiments. Here we examine the role of CsoR in vivo by examining the impact of deletion of csoR on the host transcriptome. Methods: csoR was knocked out of M. tuberculosis H37Rv using the specialized transduction method developed by Bardarov et al (2002), followed by removal of the hygromycin marker with plasmid pYUB870. Both wild type and confirmed csoR knockout were grown in copper free Sauton's media to late log phase before harvesting for transcriptomic studies. RNA was extracted using a modified Trizol method prior to DNAse treatment and rRNA depletion. Sequencing was done on an Illumina HiSeq 2000, filtered for quality using the FASTX-Toolkit, and mapped using Bowtie, and counts per locus generated with BedTools in the Galaxy platform. Differential expression analysis was carried out in edgeR with significantly differentially expressed genes being identified as those with ≥|2| fold differential expression between ΔcsoR and wild type strains, and an FDR < 0.05. Results: We found that 223 genes were differentially expressed between the ΔcsoR and wild type strains, 52 induced and 71 repressed. Differential expression of 10 of these genes, 6 induced and 4 repressed, was confirmed by qRT-PCR using SYBR green methodology. The only copper responsive genes identified were those within the csoR operon: csoR, Rv0968, ctpV, Rv0970, suggesting that csoR may only regulate its own operon in response to copper. Genes in the RicR regulon, another copper responsive transcriptional regulator, were not significantly differentially expressed, but some of these copper inducible genes were slightly down regulated suggesting that copper levels may be lower in the mutant strain as compared to wild type. Notably, 44 of the 48 members of the dosR regulon, responsive to hypoxic and NO stress, were induced in the mutant vs wild type suggesting that csoR is necessary for maintaining homeostasis, likely through copper regulation, within the cell. Conclusions: We have shown that CsoR is likely only directly regulating its own operon in response to copper, however it is required to maintain homeostasis, preventing a hypoxia-type stress response in the absense of copper.
2016-11-01 | GSE74323 | GEO
Project description:Copper is a trace metal that is necessary for all organisms but toxic when present in excess. Different mechanisms to avoid copper toxicity have been reported to date in pathogenic organisms such as Cryptococcus neoformans and Candida albicans. However, little if anything is known about pathogenic protozoans despite their importance in human and veterinary medicine. Naegleria fowleri is a free-living amoeba that occurs naturally in warm fresh water and can cause a rapid and deadly brain infection called primary amoebic meningoencephalitis (PAM). Here, we describe the mechanisms employed by N. fowleri to tolerate high copper concentrations, which include various strategies such as copper efflux mediated by a copper-translocating ATPase and upregulation of the expression of antioxidant enzymes and obscure hemerythrin-like and protoglobin-like proteins. The combination of different mechanisms efficiently protects the cell and ensures its high copper tolerance, which can be advantageous both in the natural environment and in the host. Nevertheless, we demonstrate that copper ionophores are potent antiamoebic agents; thus, copper metabolism may be considered a therapeutic target.
2021-05-19 | PXD018807 | Pride
Project description:Copper is an essential component of cytochrome C oxidase (i.e. complex IV of the electron transport chain), and is thus critical for the survival of aerobic organisms. If copper is not properly regulated in the body however, it can be extremely cytotoxic and genetic mutations that compromise copper homeostasis result in severe clinical phenotypes. Understanding how cells maintain optimal copper levels is therefore highly relevant to human health. We found that addition of copper to culture medium leads to increased respiratory growth of yeast, a phenotype which we then systematically and quantitatively measured in 5050 homozygous diploid deletion strains using microarrays.
2013-05-23 | GSE47175 | GEO
Project description:Copper (Cu) homeostasis is critical to the health of most organisms, and is thus tightly regulated by several highly conserved processes. Using the unique genomic tools available in yeast, we have expanded current knowledge of these processes by identifying 237 genes important for Cu-dependent growth. 116 of these genes, when deleted, decreased Cu-dependent respiratory growth. The remaining 121 genes, when deleted, produced respiratory growth defects that were specifically rescued by addition of Cu. Among the genes identified by our screen are known regulators of copper homeostasis, genes required to maintain low vacuolar pH, and genes where evidence supporting a functional link with Cu has been heretofore lacking. Many genes identified are not only conserved in man, but also associated with diseases spanning a variety of clinical phenotypes. We demonstrate that the approved drug disulfiram rescues Cu-deficiencies of both environmental and genetic origin, thus underscoring a potential paradigm for treating the broad spectrum of Cu-related disease in man.
2013-05-19 | E-MEXP-3884 | biostudies-arrayexpress
Project description:High levels of copper are toxic and therefore bacteria must limit free intracellular levels to prevent cellular damage. In this study, we show that a number of pneumococcal genes are differentially regulated by copper, including an operon encoding a CopY regulator, a protein of unknown function (CupA) and a P1-type ATPase, CopA, which is conserved in all sequenced Streptococcus pneumoniae strains. Transcriptional analysis demonstrated that the cop operon is induced by copper in vitro, repressed by the addition of zinc and is autoregulated by the copper-responsive CopY repressor protein. We also demonstrate that the CopA ATPase is a major pneumococcal copper resistance mechanism and provide the first evidence that the CupA protein plays a role in copper resistance. Our results also show that copper homeostasis is important for pneumococcal virulence as the expression of the cop operon is induced in the lungs and nasopharynx of intranasally infected mice, and a copA(-) mutant strain, which had decreased growth in high levels of copper in vitro, showed reduced virulence in a mouse model of pneumococcal pneumonia. Furthermore, using the copA(-) mutant we observed for the first time in any bacteria that copper homeostasis also appears to be required for survival in the nasopharynx. This SuperSeries is composed of the SubSeries listed below.
2011-07-10 | GSE30415 | GEO
Project description:Saccharomyces cerevisiae is exposed to freeze-thaw stress in commercial processes including frozen dough baking. The cell viability and fermentation activity after freeze-thaw were dramatically decreased due to freeze-thaw injury. Because freeze-thaw injury involves complex phenomena, the mechanisms of it are not fully understood. We attempted to analyze the mechanisms of freeze-thaw injury by indirect gene expression analysis during post-thaw incubation after freeze-thaw treatment using DNA microarray profiling. The results showed that a high frequency of the genes involved in the homeostasis of metal ions were up-regulated depending on the freezing period. The phenotype of the deletion mutants of the up-regulated genes extracted by indirect gene expression analysis was assessed. The deletion strains of the MAC1 and CTR1 genes involved in copper ion homeostasis exhibited freeze-thaw sensitivity, suggesting that copper ion homeostasis is required for freeze-thaw tolerance. Supplementation with copper ions during post-thaw incubation increased intracellular superoxide dismutase activity. Inverse correlated with intracellular superoxide dismutase activity, intracellular levels of reactive oxygen species were decreased. Moreover, cell viability increased by supplementation with copper ions under specific assessment conditions. This study suggested that insufficiency of copper ion homeostasis may be one of the causes of freeze-thaw injury.
2009-08-31 | GSE15461 | GEO
Project description:Whole genome transcriptional profiling was used to characterize the response of Lactobacillus plantarum WCFS1 human isolate during challenge with gallic acid (GA). Twelve independent experiments were performed and mixed at random in groups of four for total of three RNA samples. The transcriptional profile reveals a massive induction of genes involved in transport and decarboxilation of gallic acid.
2015-10-15 | GSE56997 | GEO
Project description:Saccharomyces cerevisiae is exposed to freeze-thaw stress in commercial processes including frozen dough baking. The cell viability and fermentation activity after freeze-thaw were dramatically decreased due to freeze-thaw injury. Because freeze-thaw injury involves complex phenomena, the mechanisms of it are not fully understood. We attempted to analyze the mechanisms of freeze-thaw injury by indirect gene expression analysis during post-thaw incubation after freeze-thaw treatment using DNA microarray profiling. The results showed that a high frequency of the genes involved in the homeostasis of metal ions were up-regulated depending on the freezing period. The phenotype of the deletion mutants of the up-regulated genes extracted by indirect gene expression analysis was assessed. The deletion strains of the MAC1 and CTR1 genes involved in copper ion homeostasis exhibited freeze-thaw sensitivity, suggesting that copper ion homeostasis is required for freeze-thaw tolerance. Supplementation with copper ions during post-thaw incubation increased intracellular superoxide dismutase activity. Inverse correlated with intracellular superoxide dismutase activity, intracellular levels of reactive oxygen species were decreased. Moreover, cell viability increased by supplementation with copper ions under specific assessment conditions. This study suggested that insufficiency of copper ion homeostasis may be one of the causes of freeze-thaw injury. Total RNA was extracted from the stress-treated yeast cells by using a hot phenol method. Poly(A)+ RNA was enriched from total RNA by using an Oligotex dT30 (Super) mRNA purification kit (Takara Bio, Ohtsu, Japan). cDNA synthesis, cRNA synthesis, and labeling were performed according to the Affymetrix user’s manual (Affymetrix, Santa Clara, USA). Biotinyated cRNA was fragmented and then used as a probe.Affimetrix Yeast Genome 2.0 arrays (Affymetrix) were used as DNA microarrays. All experiments were done in triplicate independently.
2009-08-31 | E-GEOD-15461 | biostudies-arrayexpress
Project description:Whole genome transcriptional profiling was used to characterize the response of Lactobacillus plantarum WCFS1 human isolate during challenge with 1.5 mM gallic acid (GA). Twelve independent experiments were performed and mixed at random in groups of four for total of three RNA samples. The transcriptional profile reveals a massive induction of genes involved in transport and decarboxilation of gallic acid.
2015-10-15 | GSE63728 | GEO