Uropathogenic versus Urocolonizing Escherichia coli
Ontology highlight
ABSTRACT:
ORGANISM(S): Escherichia Coli
TISSUE(S): Bacterial Cells
PROVIDER: ST001244 | MetabolomicsWorkbench |
REPOSITORIES: MetabolomicsWorkbench
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| mwtab | Other |
Items per page: 5 1 - 1 of 1 |
Similar Datasets
Project description:DNA microarray experiments were used to compare gene expression profiles of untreated and 5-azacytidine treated Escherichia coli at both logarithmic phase and early stationary phase The goal was to determine the effect of cytosine DNA methylation loss on gene expression (5-azacytidine is a methylation inhibitor)
2016-09-24 | GSE73707 | GEO
Project description:Gene expression profiling of EHEC and its luxS-deficient mutant strain which cannot produce autoinducer-2 molecule at the late log-phase in 0.6M NaCl LB broth (osmotic stress condition) against controls grown under normal osmotic condition (LB broth)
2017-10-30 | E-MTAB-5757 | biostudies-arrayexpress
Project description:Both ppGpp and pppGpp are thought to function collectively as second messengers for many complex cellular responses to nutritional stress throughout biology. There are few indications that their regulatory effects might be different; however, this question has been largely unexplored for lack of an ability to experimentally manipulate the relative abundance of ppGpp and pppGpp. Here, we achieve preferential accumulation of either ppGpp or pppGpp with Escherichia coli strains through induction of different Streptococcal (p)ppGpp synthetase fragments. In addition, expression of E. coli GppA, a pppGpp 5'-gamma phosphate hydrolase that converts pppGpp to ppGpp, is manipulated to fine tune differential accumulation of ppGpp and pppGpp. In vivo and in vitro experiments show that pppGpp is less potent than ppGpp with respect to regulation of growth rate, RNA/DNA ratios, ribosomal RNA P1 promoter transcription inhibition, threonine operon promoter activation and RpoS induction. To provide further insights into regulation by (p)ppGpp, we have also determined crystal structures of E. coli RNA polymerase-σ(70) holoenzyme with ppGpp and pppGpp. We find that both nucleotides bind to a site at the interface between β' and ω subunits.
| S-EPMC3695517 | biostudies-literature
Project description:The present study investigated the role(s) of RNase I (encoded by the rna gene) in Escherichia coli by comparative gene expression analysis of an rna mutant and the isogenic wild-type E. coli strain BW25113. The transcriptomic analysis aims to provide mechanistic insight into aberrant phenotypes observed in the RNase I-deficient mutant.
2020-01-04 | E-MTAB-6095 | biostudies-arrayexpress
Project description:We studied the proteome changes in Escherichia coli growing in rich media, and compared the changes between exponential phase cells and those underwent sudden carbon starvations.
2021-03-09 | PXD024151 | Pride
Project description:The experiment contains ChIP-seq data for Escherichia coli strain RPB104 hns::kan. The strain was grown at 37 degrees in LB medium to stationary phase and crosslinked with 1 % (v/v) formaldehyde. After sonication, to break open cells and fragment DNA, immunoprecipitations were done using anti-FLAG antibodies. Libraries were prepared using DNA remaining after immunoprecipitation.
2021-03-01 | E-MTAB-8778 | biostudies-arrayexpress
Project description:We compared PCR amplification of 9 enterohemorrhagic Escherichia coli virulence factors among 40 isolates (21 O/H antigenicity classes) with DNA hybridization. Both methods showed 100% of the chromosomal and phage genes: eae, stx, and stx2. PCR did not detect 4%-20% of hybridizable plasmid genes: hlyA, katP, espP, toxB, open reading frame (ORF) 1, and ORF2.
| S-EPMC2828064 | biostudies-literature
Project description:Expression of bacterial genes takes place under the control of RNA polymerase with exchangeable ?-subunits and multiple transcription factors. A typical promoter region contains one or several overlapping promoters. In the latter case promoters have the same or different ?-specificity and are often subjected to different regulatory stimuli. Genes, transcribed from multiple promoters, have on average higher expression levels. However, recently in the genome of Escherichia coli we found 78 regions with an extremely large number of potential transcription start points (promoter islands, PIs). It was shown that all PIs interact with RNA polymerase in vivo and are able to form transcriptionally competent open complexes both in vitro and in vivo but their transcriptional activity measured by oligonucleotide microarrays was very low, if any. Here we confirmed transcriptional defectiveness of PIs by analyzing the 5'-end specific RNA-seq data, but showed their ability to produce short oligos (9-14 bases). This combination of functional properties indicated a deliberate suppression of transcriptional activity within PIs. According to our data this suppression may be due to a specific conformation of the DNA double helix, which provides an ideal platform for interaction with both RNA polymerase and the histone-like nucleoid protein H-NS. The genomic DNA of E.coli contains therefore several dozen sites optimized by evolution for staying in a heterochromatin-like state. Since almost all promoter islands are associated with horizontally acquired genes, we offer them as specific components of bacterial evolution involved in acquisition of foreign genetic material by turning off the expression of toxic or useless aliens or by providing optimal promoter for beneficial genes. The putative molecular mechanism underlying the appearance of promoter islands within recipient genomes is discussed.
| S-EPMC3661553 | biostudies-literature
Project description:In order to determine whether dis-regulation of a genetic pathway could explain the increased apoptosis of parp-2-/- double positive thymocytes, the gene expression profiles in double positive thymocytes derived from wild-type and parp-2-/- mice were analysed using Affymetrix oligonucleotide chips (mouse genome 430 2.0).
2007-05-23 | E-MEXP-755 | biostudies-arrayexpress
Project description:The Planctomycetes have unique cell architectures with heavily invaginated membrane networks, as here confirmed by three-dimensional models reconstructed from FIB-SEM images of Tuwongella immobilis and Gemmata obscuriglobus. We studied the subcellular proteomes of T. immobilis, and for comparison Escherichia coli, by differential solubilisation followed by LC-MS/MS analysis. More than one thousand proteins were identified in each species. The first Tris-soluble fraction contained mostly cytoplasmic proteins, whereas membrane proteins dominated the second Triton X-100 cell extract. About 50 proteins were exclusive to the third SDS-soluble extract in E. coli, mostly outer membrane and cell surface proteins. A 5-fold higher number of proteins were identified in this fraction in T. immobilis, including predicted cell surface proteins with a prepilin cleavage motif or a Planctomycetes-specific signal peptide. Surprisingly, 50% of the predicted cytoplasmic proteins were exclusively associated with the SDS-soluble protein fraction in T. immobilis. Proteins involved in signal transduction pathway and transcriptional regulation were highly overrepresented in this set, as were also enzymes involved in DNA repair and processing of stable RNAs. Some of these proteins are unique to the Planctomycetes, while others have evolved by gene duplication and domain shuffling. In cases where the paralogs showed different fractionation patterns, it was the most divergent gene copy that was uniquely associated with the SDS-soluble fraction. These results are consistent with the hypothesis that gene duplication and domain shuffling underlie the evolution of new gene functions in the Planctomycetes. We further suggest that repair and recycling of “ageing” molecules play a more important role in the Planctomycetes than in other bacteria due to their large cell sizes, long generation times and life styles.
2021-04-06 | PXD022526 | Pride