The transcriptomic response of E. coli to triclosan exposure
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ABSTRACT:
ORGANISM(S): Escherichia coli
PROVIDER: GSE15059 | GEO | 2009/08/20
SECONDARY ACCESSION(S): PRJNA114827
REPOSITORIES: GEO
Similar Datasets
Project description:The gene expression profile of E. coli K-12 MG1655 grown in minimal medium treated with 0.12 mg/L of the biocide triclosan has been analysed using whole genome oligonucleotide microarrays. "Control" RNA was isolated from three independently grown 50ml MOPS minimal media cultures of E. coli K-12 MG1655. âTestâ RNA was isolated from three independently grown 50ml MOPS minimal cultures of E. coli K-12 MG1655, to which was added 0.12 mg/L of triclosan after reaching mid-logarithmic growth phase (OD600 ~ 0.7 +/- 0.02). Keywords: dose response Cy5-labelled cDNA probes were synthesised from three independent biological extractions of RNA from E. coli MG1655 unexposed to triclosan. Cy3-labelled cDNA probes were synthesised from three independent biological extractions of RNA from E. coli MG1655 exposed to 0.12 mg/L of triclosan. A dye-swap control was also included, whereupon the control cDNA probes were labelled with Cy3 and the test cDNA probes labelled with Cy5. Probes were mixed to allow comparison of the control and test expression profiles and hybridised onto an E. coli spotted oligonucleotide array.
2010-10-08 | E-GEOD-15059 | biostudies-arrayexpress
Project description:The gene expression profile of E. coli K-12 MG1655 grown in minimal medium supplemented with elevated copper concentrations (as copper-glycine) has been analysed using whole genome oligonucleotide microarrays. “Pool” RNA was isolated from five independently grown 50ml DMA cultures of E. coli K-12 MG1655. “Test” RNA was isolated from three independently grown 50ml DMA cultures of E. coli K-12 MG1655, for each growth condition (no added CuSO4, or supplemented with either 0.75mM or 2mM copper glycine). A sample of each culture was taken at mid to late exponential growth phase at OD600 0.8 (measured using a Pharmacia Biotech Ultrospec 2000 in a cuvette with a path length of 10mm). Keywords: dose response
2004-09-22 | GSE1780 | GEO
Project description:The gene expression profile of E. coli K-12 MG1655 grown in minimal medium supplemented with elevated copper concentrations (as copper-glycine) has been analysed using whole genome oligonucleotide microarrays. â??Poolâ?? RNA was isolated from five independently grown 50ml DMA cultures of E. coli K-12 MG1655. â??Testâ?? RNA was isolated from three independently grown 50ml DMA cultures of E. coli K-12 MG1655, for each growth condition (no added CuSO4, or supplemented with either 0.75mM or 2mM copper glycine). A sample of each culture was taken at mid to late exponential growth phase at OD600 0.8 (measured using a Pharmacia Biotech Ultrospec 2000 in a cuvette with a path length of 10mm).
2010-06-05 | E-GEOD-1780 | biostudies-arrayexpress
Project description:Our focus of this study is to determine the differential expression of genes related to uptake and degradation of nitrogenous compounds in E. coli colonizing the mouse intestine as compared to E. coli grown in minimal medium in vitro. We colonized CD-1 male mice with E. coli MG1655 StrR wild type and extracted the total RNA from mouse cecal mucus (GSE217743). We also colonized CD-1 male mice with E. coli MG1655 ∆glnG StrR CamR and extracted the total RNA from mouse cecal mucus. We grew E. coli MG1655 StrR wild type in MOPS minimal medium containing high nitrogen (10 mM NH4Cl) and low nitrogen (3 mM NH4Cl) and extracted the total RNA from exponential phase and stationary phase culture. We also grew E. coli MG1655 ∆glnG StrR CamR in MOPS minimal medium containing low nitrogen (3 mM NH4Cl) and extracted the total RNA from exponential phase culture. The extracted RNA samples were sequenced, and differential expression analysis was done to determine the genes related to uptake and degradation of nitrogenous compounds that are important for E. coli colonization. Our results indication nitrogen is not limiting for E. coli in the intestine and genes related to uptake and degradation of several aminoacids, di- and tripeptides, aminosugars, ethanolamine, urea among others are upregualated in the mouse intestine as compared to invitro culture grown in high nitrogen conditions.
2024-01-29 | GSE241658 | GEO
Project description:E. coli K-12 MG1655 was grown on M9 minimal media supplemented with 0.2% w/v glucose, fructose, or acetate. The goal of this study was to determine differentially expressed genes in the different media conditions.
2018-02-02 | GSE108871 | GEO
Project description:Transcription profiling of wild type E. coli MG1655, intestine-adapted E. coli MG1655star, and E. coli MG1655 flhD mutant grown on glucose, mannose, and mucus. We previously isolated a spontaneous mutant of E. coli K-12, strain MG1655, following passage through the streptomycin-treated mouse intestine, which has colonization traits superior to the wild-type parent strain (Leatham, et. al., 2005, Infect Immun 73:8039-49) The intestine-adapted strain (E. coli MG1655star) grew faster on several different carbon sources compared to the wild-type and was non-motile due to deletion of the flhD gene. To further characterize E. coli MG1655star, we used several high-throughput genomic approaches. Whole-genome pyrosequencing did not reveal any changes on its genome, aside from the deletion at the flhDC locus, that could explain the colonization advantage of E. coli MG1655star. Microarray analysis revealed modest, yet significant induction of catabolic gene systems across the genome in both E. coli MG1655star and the isogenic flhD mutant. Catabolome analysis with Biolog GN2 Microplates revealed an enhanced ability of both E. coli MG1655star and the isogenic flhD mutant to oxidize a wide variety of carbon sources. The results show that intestine-adapted E. coli MG1655star is more fit than the wild-type for intestinal colonization because loss of FlhD results in elevated expression of genes involved in carbon and energy metabolism, leading to more efficient carbon source utilization, which results in a higher population size in the intestine. Hence mutations that enhance metabolic efficiency confer a colonization advantage. Three strains were profiled: E. coli MG1655 wildtype, E. coli flhD, and an intestine adapted strain, MG1655star, derived from the wildtype and isolated from feces after 15 days in the streptomycin treated mouse intestine, which proved to be a better colonizer than the wildtype, were grown on MOPS minimal medium containing 0.2% glucose or mannose, or mucus (10 mg/ml) and RNA was extracted from logarithmic phase cultures, and also from mucus grown cells in late log phase.
2010-11-04 | E-GEOD-25106 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level in E. coli K-12 MG1655 in glucose M9 minimal media with/without heatshock
2013-06-20 | GSE42675 | GEO
Project description:Investigation of whole genome gene expression level in E. coli K-12 MG1655 in glucose M9 minimal media with/without heatshock A six chip study using total RNA recovered from E. coli K-12 MG1655 grown up to OD600nm 0.6 (mid-exponential phase) in M9 minimal media supplemented with 0.2% glucose with/without heatshock in 42oC. The high-density oligonucleotide tiling arrays used were consisted of 371,034 oligonucleotide probes with 50-bp length that are spaced 25 bp apart across the E. coli genome (NimbleGen). Experiments were performed with three biological replicates.
2013-06-20 | E-GEOD-42675 | biostudies-arrayexpress
Project description:Transcriptome profiling of E. coli MG1655, E. coli EDL933, E. coli ECOR26, and E. coli Nissle 1917 grown on mouse cecal mucus as carbon source The carbon sources that support growth of pathogenic E. coli O157:H7 in the mammalian intestine have not previously been investigated. In vivo, pathogenic E. coli EDL933 primarily grows as dispersed single cells within the mucus layer that overlies the mouse cecal epithelium. We therefore compared the pathogen and commensal E. coli MG1655 for their mode of metabolism in vitro on a mixture of the sugars known to be present in cecal mucus and found that the two strains used the thirteen sugars in a similar order and co-metabolized as many as nine sugars at a time. We conducted a systematic mutational analysis of E. coli EDL933 and E. coli MG1655 with lesions in the pathways used for catabolism of thirteen mucus-derived sugars and five other compounds for which the corresponding gene system was induced in the transcriptome of cells grown on cecal mucus. Each of 18 catabolic mutants in both genetic backgrounds was fed to streptomycin-treated mice together with the respective wildtype parent strain and their colonization was monitored in fecal plate counts. None of the mutations corresponding to the five compounds not found in mucosal polysaccharides resulted in colonization defects. Based on the mutations that caused colonization defects, we determined that both E. coli EDL933 and E. coli MG1655 used arabinose, fucose, and N-acetylglucosamine in the intestine. In addition, E. coli EDL933 used galactose, hexuronates, mannose and ribose, whereas E. coli MG1655 used gluconate and N-acetylneuraminic acid. The colonization defects of six catabolic lesions were found to be additive in E. coli EDL933, but not E. coli MG1655. The data indicate that pathogenic E. coli EDL933 uses sugars that are not used by commensal E. coli MG1655 to colonize the mouse intestine. The results suggest a strategy whereby invading pathogens gain advantage by simultaneously consuming several sugars that may be available because they are not consumed by the commensal intestinal microbiota. Keywords: growth condition: carbon source was mouse cecal mucus E. coli strains were grown on MOPS minimal medium containing 10 mg/ml of mucus or 0.2% glucose in 10 ml standing culture in testtubes and harvested at OD600 = 0.4.
2008-04-25 | E-GEOD-11254 | biostudies-arrayexpress
Project description:Expression profiling of wild type and purR deletion strains of E. coli K-12 MG1655 under both M9 minimal media and addition of adenine.
2011-06-14 | GSE26588 | GEO