ChemProp2-Xenobiotic Metabolism
Ontology highlight
ABSTRACT:
INSTRUMENT(S): LTQ Orbitrap Elite, Q Exactive
ORGANISM(S): Bacillus Subtilis (ncbitaxon:1423)
SUBMITTER: 
Daniel Petras
PROVIDER: MSV000089466 | MassIVE | Fri May 13 06:27:00 BST 2022
REPOSITORIES: MassIVE
Similar Datasets
Project description:Chemical Proportionality Experiment of B.subtilis with antibiotics & pesticides such as Sulfamethoxazole, sulfadimethoxine and asulam to look for potential biotransformation
2022-05-13 | MSV000089466 | GNPS
Project description:Chemical Proportionality Experiment of B.subtilis and E.coli added with pooled antibiotics (Sulfamethoxazole, sulfadimethoxine, cyproconazole and asulam) to look for potential biotransformation.
2022-05-24 | MSV000089534 | MassIVE
Project description:Chemical Proportionality Experiment of B.subtilis and E.coli added with pooled antibiotics (Sulfamethoxazole, sulfadimethoxine, cyproconazole and asulam) to look for potential biotransformation.
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Project description:Animals have developed extensive mechanisms of response to xenobiotic chemical attacks. Although recent genome surveys have suggested a broad conservation of the chemical defensome across metazoans, global gene expression responses to xenobiotics are not known in most invertebrates. Here, using high density tiling arrays with over 2 million probes, we explored genome-wide gene expression in the tunicate Oikopleura dioica in response to two model xenobiotic chemicals – the carcinogenic polycyclic aromatic hydrocarbon benzo[a]pyrene (BaP) the pharmaceutical compound Clofibrate (Clo). The genotoxic compound BaP induced xenobiotic biotransformation and oxidative stress responsive genes, as in vertebrates. Notable exceptions were genes of the aryl hydrocarbon receptor (AhR) signaling pathway. Clo also affected the expression of many biotransformation genes and markedly repressed genes involved in energy metabolism and muscle contraction pathways. Oikopleura appears to have basic defensome toolkit consisting of phase I, phase II and phase III biotransformation genes.
2013-02-05 | GSE33818 | GEO
Project description:Biotransformation of soil organochlorine pesticides (OCP) is often impeded by a lack of nutrients relevant for bacterial growth and/or co-metabolic OCP biotransformation. By providing space-filling mycelia, fungi promote contaminant biodegradation by facilitating bacterial dispersal and the mobilization and release of nutrients in the mycosphere. We here tested whether mycelial nutrient transfer from nutrient-rich to nutrient-deprived areas facilitates bacterial OCP degradation in a nutrient-deficient habitat. The legacy pesticide hexachlorocyclohexane (HCH), a non-HCH-degrading fungus (Fusarium equiseti K3), and a co-metabolically HCH-degrading bacterium (Sphingobium sp. S8) isolated from the same HCH-contaminated soil were used in spatially structured model ecosystems. Using 13C-labelled fungal biomass and protein-based stable isotope probing (protein-SIP), we traced the incorporation of 13C fungal metabolites into bacterial proteins while simultaneously determining the biotransformation of the HCH isomers. The relative isotope abundance (RIA, 7.1 – 14.2%), labeling ratio (LR, 0.13 – 0.35), and the shape of isotopic mass distribution profiles of bacterial peptides indicated the transfer of 13C-labeled fungal metabolites into bacterial proteins. Distinct 13C incorporation into the haloalkane dehalogenase (linB) and 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase (LinC), as key enzymes in metabolic HCH degradation, underpin the role of mycelial nutrient transport and fungal-bacterial interactions for co-metabolic bacterial HCH degradation in heterogeneous habitats. Nutrient uptake from mycelia increased HCH removal by twofold as compared to bacterial monocultures. Fungal-bacterial interactions hence may play an important role in the co-metabolic biotransformation of OCP or recalcitrant micropollutants (MPs).
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Project description:The tetracycline antibiotics are widely used in biomedical research as mediators of inducible gene expression systems. Despite many known effects of tetracyclines on mammalian cells -- including inhibition of the mitochondrial ribosome -- there have been few reports on potential off-target effects at concentrations commonly used in inducible systems. Here, we report that in human cell lines, commonly used concentrations of doxycycline change gene expression patterns and concomitantly shift metabolism towards a more glycolytic phenotype, evidenced by increased lactate secretion and reduced oxygen consumption. We also show that these concentrations are sufficient to slow proliferation and alter cell cycle progression in vitro. These findings suggest that researchers using doxycycline in inducible expression systems should design appropriate controls to account for potential confounding effects of the drug on cellular metabolism. Total RNA was extracted from MCF12A cells treated with either vehicle control or Dox at 1 ug/mL. The experiment was performed in biological triplicate. Microarray results were processed using the RMA method.
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Project description:The synthesis mechanisms and function evaluation of selenium(Se)-enriched microorganism remain relatively unexplored. We here report the Se biotransformation by A. oryzae A02. Comparative RNA-Seq analysis revealed the upregulation of functional genes implicated in selenium transformation, activating multiple potential pathways for selenium reduction. The assimilatory and dissimilatory reductions of Se oxyanions engaged numerous parallel and interconnected pathways, manifesting a harmonious equilibrium in overall Se biotransformation in A. oryzae A02.
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Project description:Animals have developed extensive mechanisms of response to xenobiotic chemical attacks. Although recent genome surveys have suggested a broad conservation of the chemical defensome across metazoans, global gene expression responses to xenobiotics are not known in most invertebrates. Here, using high density tiling arrays with over 2 million probes, we explored genome-wide gene expression in the tunicate Oikopleura dioica in response to two model xenobiotic chemicals – the carcinogenic polycyclic aromatic hydrocarbon benzo[a]pyrene (BaP) the pharmaceutical compound Clofibrate (Clo). The genotoxic compound BaP induced xenobiotic biotransformation and oxidative stress responsive genes, as in vertebrates. Notable exceptions were genes of the aryl hydrocarbon receptor (AhR) signaling pathway. Clo also affected the expression of many biotransformation genes and markedly repressed genes involved in energy metabolism and muscle contraction pathways. Oikopleura appears to have basic defensome toolkit consisting of phase I, phase II and phase III biotransformation genes. Exposure of about 130 four-days-old animals in 1L seawater in glass beakers. Pooled animals used, no replicates. DMSO Treatments: -Clofibrate (Clo) (Sigma-Aldrich, St. Louis, MO): 1 µM and 5 µM. -Benzo[a]pyrene (BaP (Sigma-Aldrich): 0.2 µM and 1 µM - Controls received 1 ml Dimethyl sulfoxide (DMSO). -The animals kept at room temperature and harvested after 10 hrs and frozen. -Total RNA was isolated from the pooled animals using the RNeasy Mini Kit according to manufacturer’s protocols (QIAGEN, Hilden, Germany). - 5 µg total RNA was converted to dscDNA using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen, Carlsbad, CA), and dscDNA samples were submitted for microarray analysis. BaP and Clo treated samples were labeled using Cy3-coupled random nonamers and DMSO controls were labeled using Cy5-coupled random nonamers. Total 4 hybridizations for the 8 samples (single hybridization for each treatment and DMSO control pair), no replicates.
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