Identification and metabolism of naturally prevailing microorganisms in zinc and copper minerals processing
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB42463 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR5100010_1.fastq.gz | Fastqsanger.gz | |||
| ERR5100010_2.fastq.gz | Fastqsanger.gz | |||
| ERR5100011_1.fastq.gz | Fastqsanger.gz | |||
| ERR5100011_2.fastq.gz | Fastqsanger.gz | |||
| ERR5100012_1.fastq.gz | Fastqsanger.gz |
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Project description:Naturally prevailing microorganisms in zinc and copper minerals processing
| PRJEB41552 | ENA
Project description:In this study we used a transcriptomic approach to study the molecular determinants of the synergy between copper and fluconazole, in Candida glabrata, the second most frequent cause of invasive candidiasis. We demonstrate that copper acts together with fluconazole by downregulating three distinct pathways: azole efflux, ergosterol biosynthesis and zinc homeostasis. Coincidently, all these pathways are important for C. glabrata to cope with fluconazole stress. Therefore, when copper and fluconazole are combined cells fail to detoxify this drug and accumulate toxic methylated intermediates of sterol metabolism. This accumulation, possibly together with copper-induced lipid damages, should affect the activity of plasma membrane transporters, which impedes zinc uptake, leading to zinc depletion
2022-06-01 | GSE162741 | 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: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:We studied the influence of copper in physiological and morphological differentiation of Streptomyces coelicolor. We demonstrate differences in phenotype (germination, growth rate, antibiotic production) and genetic expression between a strain mutated at copper chaperone CopZ (SCO2730::Tn5062), the wild-type strain and a wild-type strain sporulated in a media with 80µM CuSO4. These differences are correlated with the cytosolic copper. Our results demonstrate a pleiotropic effect of copper modulating S. coelicolor development.
2018-12-31 | GSE111126 | GEO
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 is both an essential enzyme cofactor and an antimicrobial agent deployed by the host immune system to eradicate micro-organisms. The epidemic community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) lineage USA300 carries mobile genetic elements that encode copX/B and copL, conferring hyper-resistance to copper, but the role of CopL beyond extracellular copper sequestration remains unclear. We have combined RNA sequencing with targeted metabolite assays under microaerobic conditions, more reflective of host environments, to define key copper induced responses in WT and copL mutant strains. Subinhibitory copper exposure in microaerobic conditions triggered a distinctive transcriptional response across multiple biological functions. Unlike previous studies, copper exposure did not induce an oxidative stress response. Instead, classical copper resistance, teichoic acid modification, immune-evasion factors and core metabolic genes were induced, while genes for stress responses, metal homeostasis and virulence were repressed. Gene set enrichment analysis (GSEA) identified regulation by multiple global regulators, e.g. SigB, CodY, CcpA, Agr and Sae. Copper exposure affected metabolism, redirecting pyruvate flux toward acetoin and lactate production rather than acetate, accompanied by coordinated shifts in TCA cycle and amino acid pathways, including glutamate accumulation. Inactivation of copL revealed a distinct adaptive response, with strong induction of nitrogen metabolism genes and nitrite reduction. Together, these data show that copper functions as a regulatory signal, triggering coordinated transcriptional and metabolic remodelling that potentiates S. aureus fitness in the host.
2026-06-18 | GSE335600 | GEO
Project description:Lovastatin and other statins inhibit HMG-CoA reductase, which carries out an early step in the sterol biosynthesis pathway. Statins lower cholesterol and are widely prescribed to prevent heart disease, but like many drugs, they can interact with nutritionally acquired metabolites. To probe these interactions, we explored the effect of a diverse library of metabolites on statin effectiveness using a Saccharomyces cerevisiae model. In yeast, treatment with lovastatin results in reduced growth. We combined lovastatin with the library of metabolites and found that copper and zinc ions impaired the ability of the statin to inhibit yeast growth. Using an integrated genomic and metabolomic approach, we found that lovastatin plus metal synergistically upregulated some sterol biosynthesis genes. This altered pattern of gene expression resulted in greater flux through the sterol biosynthesis pathway and an increase in ergosterol levels. Each sterol intermediate level was correlated with expression of the upstream gene. Thus, the ergosterol biosynthetic response induced by statin is enhanced by copper and zinc. In cultured mammalian cells, these metals also rescued statin growth inhibition. Because copper and zinc impair the ability of statin to reduce sterol biosynthesis, dietary intake of these metals could have clinical relevance for statin treatment in humans.
2010-10-29 | GSE25004 | GEO
Project description:A systems level analysis of Chromochloris zofingiensis during copper, iron, and zinc deficiencies when grown photoautotrophically and mixotrophically in a revised TP medium with special K mineral nutrients.
2024-11-08 | MSV000096362 | MassIVE
Project description:The clinical manifestations of Wilson disease (WD) are related to copper accumulation in the liver and brain, but little is known about the role of other organs expressing the ATP7B copper transporter on the metabolic changes characterizing WD. To examine the metabolic and morphological consequences of intestine Atp7b inactivation in absence of hepatic copper accumulation, we generated a new mouse strain, the Atp7bΔIEC mouse and characterized its phenotype over a time-course study. Atp7bΔIEC mice were generated using B6.Cg-Tg(Vil1-cre)997Gum/J mice from the Jackson Laboratory and Atp7bLox/Lox mice. Cre-mediated removal of a 1.6-kb fragment in exon 2 results in enterocyte-specific Atp7b inactivation. Atp7bΔIEC mice were compared to wildtype mice with same genetic background (iWT). The Atp7b null global knockout (Atp7b -/-) on a C57Bl/6 background was previously generated and compared to respective WT. Mice were studied at 9, 16, 24, and 30 weeks of age. Liver and intestine histology, lipid metabolism parameters, and hepatic copper quantification were assessed. Transcriptome analysis in Atp7bΔIEC mice revealed changes in genes involved in AMPK signaling, fatty acid metabolism and cell cycle both in the intestinal epithelial cells and in the liver. No changes in hepatic and enterocyte copper levels were seen in Atp7bΔIEC livers, whereas, as expected, hepatic copper was 20-40 times higher in Atp7b -/- mice compared to WT mice. Intestine-specific Atp7b deficit affects systemic metabolic pathways independently from hepatic copper accumulation indicating evidence that WD phenotype is affected by organ-specific ATP7B variants.
2025-06-01 | GSE279388 | GEO