SRNA-mediated regulation of P-fimbriae phase variation in intracellular uropathogenic Escherichia coli
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2000
ORGANISM(S): Escherichia coli
SUBMITTER: surabhi khandige
PROVIDER: E-MTAB-3498 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Transcriptional analysis of UTI89 - uropathogenic E.coli (UPEC) strain grown in urine/Luria bertani medium culture in vitro as well as during three distinct phases of UPEC bladder infection: intracellular growth, filament formation and filament reversal. UTI89 was used to infect a bladder epithelial cell line cultured within a dynamic flow chamber system and harvested at particular stages of its pathogenecity cascade. Total RNA was processed and cy3 labeled for microarray analysis using Agilent custom Escherichia coli UTI89 arrays designed using E-Array.
2017-05-28 | E-MTAB-3611 | biostudies-arrayexpress
Project description:Uropathogenic Escherichia coli (UPEC) are the most common cause of urinary tract infection (UTI). UPEC normally reside in the intestine, and during establishment of UTI, it undergoes metabolic adaptations, first to urine and then upon tissue invasion to the bladder cell interior. In order to understand these adaptations, we used quantitative proteomic profiling to characterize protein expression of UPEC strain UTI89 growing in human urine and when inside J82 bladder cells. In order to facilitate detection of UPEC proteins over the excess amount of eukaryotic proteins in bladder cells, we developed a method where proteins from UTI89 grown in MOPS and urine was spiked-in to enhance detection of bacterial proteins. More than 2000 E. coli proteins were detected. During growth in urine, proteins associated with iron acquisition and several amino acid uptake and biosynthesis systems, in particular arginine metabolism, were significantly upregulated. During growth in J82 cells, proteins related to iron uptake and arginine metabolisms were upregulated together with proteins involved in sulphur compound turnover. Results suggested that UPEC experience a richer environment in bladder cells compared to urine. There was no direct correlation between upregulated proteins and proteins reported to be essential for infections, showing that upregulation during growth does not signify that the proteins are essential for growth under a condition.
2022-06-09 | PXD032049 | Pride
Project description:The method DFI-seq was developed to enable identification of differentially expressed genes in uropathogenic E. coli strain UTI89 during growth in human urine and in bladder epithelial cells. By utilising this new method, the aim was to identify novel virulence genes in UTI89. DFI-seq is a combination of differential fluorescence induction (DFI) with next-generation sequencing. DFI-seq was compared to DFI by analysing gene expression of UPEC in human urine and thereby confirming that DFI-seq gives a better overview of gene expression. DFI-seq was hereafter used to look at gene expression in UTI89 while infecting bladder epithelial cells. We demonstrate the usefulness of DFI-seq for identification of genes required for optimal growth of UPEC in human urine, as well as potential virulence genes upregulated during infection of bladder epithelial cells. DFI-seq holds potential for the study of bacterial gene expression in live-animal infection systems.
2017-05-01 | E-MTAB-5657 | biostudies-arrayexpress
Project description:In Escherichia coli, the highly conserved enzymes MiaA and MiaB mediate the sequential prenylation and methylthiolation of adenosine-37 within tRNAs that decode UNN codons. We found that MiaA, but not MiaB, is critical to the fitness and virulence of extraintestinal pathogenic E. coli (ExPEC), a major cause of urinary tract and bloodstream infections. Deletion of miaA has pleiotropic effects, attenuating bacterial fitness and virulence within diverse host environments and rendering ExPEC especially sensitive to stressors like nitrogen and oxygen radicals and osmotic shock. We find that stress can stimulate striking changes in miaA expression. To assess how changing MiaA levels affect the pathogen proteome, we used MS to analyze the proteins express by the reference ExPEC isolate UTI89 and derivatives that either lack or overexpress MiaA.
2022-02-14 | PXD024782 | Pride
Project description:While in transit within and between hosts, uropathogenic E. coli (UPEC) encounter multiple stresses, including substantial levels of nitric oxide and reactive nitrogen intermediates. Strains of UPEC become conditioned to high concentrations of acidified sodium nitrite (ASN), a model system used to generate nitrosative stress. We used microarrays to define the expression profile of UPEC that have been conditioned for growth in ASN. Experiment Overall Design: Separate colonies of the UPEC isolate UTI89 grown on LB agar plates from a -80°C freezer stock were used to start overnight shaking cultures in MES-buffered LB broth (MES-LB, pH 5.0). Each culture was then diluted 1:100 into 7 ml MES-LB with or without 3 mM ASN in loosely capped 20-by-150-mm borosilicate glass tubes and grown with shaking at 37°C. Growth was monitored by optical density until OD600 = 1.5, at which point cultures were spun down, and pellets frozen at -80°C for at least 12 h. RNA was extracted with hot phenol-chloroform and purified by CsCl centrifugation. cDNA was synthesized, fragmented, and labeled for hybridization to Affymetrix GeneChip® E. coli Genome 2.0 Arrays.
2009-03-28 | E-GEOD-15319 | biostudies-arrayexpress
Project description:Mice were infected with the cystitis isolate UTI89 transurethrally and sacrificed 28 days post infection. Total bladder RNA was harvested from mock, resolved or chronic bladder and analyzed using the mouse gene 1.0 st chips.
2014-12-06 | E-MTAB-2930 | biostudies-arrayexpress
Project description:Among the most important regulators of gene expression in bacteria are 'nucleoid-associated proteins'. These proteins alter the topology of the bound DNA by bending, wrapping or bridging it, thus having multiple effects, including transcriptional regulation, on the bacterial cell. Among the best-studied nucleoid proteins are H-NS and Fis, which bind to specific sequences on the DNA. H-NS is a global repressor of gene expression. Fis alters the global conformation of the DNA by introducing branched structures in it; but its effect on gene expression on a genomic scale remains largely unclear.<br><br>Several bacterial transcriptional regulators including H-NS and Fis have been studied using ChIP-chip. However, the higher resolution and dynamic range offered by ChIP-Seq have not been exploited for any bacterial species. By performing ChIP-Seq of these two proteins, we present the first such study in a bacterium. In addition to providing a proof-of-principle for the use of this technology for bacteria, we perform our study at multiple time-points during growth in rich medium, thus generating new insights into how these proteins function under different cellular conditions. Further, by analysing our data in conjunction with newly-generated gene expression and RNA polymerase-chromosome interaction data we provide new interpretation of the genome-scale patterns of the interactions of these proteins to the DNA.
2010-09-01 | E-MTAB-332 | biostudies-arrayexpress
Project description:Data defines for the first time a whole bladder transcriptome of UPEC cystitis in female C57BL/6 mice using genome-wide expression profiling and temporal analysis to map early host response pathways stemming from UPEC colonization We used microarrays to detail the global programme of gene expression in GBS UTI in mice over time and in UPEC UTI in mice at 24h Whole mouse bladder collected at 2h and 24h following transurethral infection for RNA extraction and hybridization on Affymetrix microarrays. Non-pooled samples were used, with one array per mouse to expand power of expression profiles. Control mice for each time point received only PBS as a mock infection. Group sizes were five mice per group, and therefore five arrays were used per group. Whole mouse bladder collected at 24h following transurethral infection for RNA extraction and hybridization on Affymetrix microarrays. Non-pooled samples were used, with one array per mouse to expand power of expression profiles. Control mice for each time point received only PBS as a mock infection. Group sizes were five mice per group, and therefore five arrays were used per group.
2012-06-30 | E-GEOD-27575 | biostudies-arrayexpress
Project description:The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing bladder. The central thesis is straightforward. The combination of microdissected tissues and FACS sorted cells plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing urogenital system. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone. The data submitted here delineates the gene expression profiles of the mesenchymal and epithelial compartments of the e13 mouse bladder. Keywords: Mouse embryonic day 13 bladder mesenchyme and epithelium. FVB/N mice were time mated. At embryonic day 13 mice were euthanized by decapitation and the bladders were microdissected, cut just above the ureters, and treated with 20 µM EDTA for 20 minutes. Mesenchymal and epithelial compartments were then separated by rimming the bladder with a needle and harvested in RLT. Total RNA was isolated for gene expression analysis using the Affymetrix MOE430 microarray chip
2009-01-16 | E-GEOD-12618 | biostudies-arrayexpress
Project description:The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing bladder. The central thesis is straightforward. The combination of micro dissected tissues and FACS sorted cells plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing urogenital system. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone. The data submitted here delineates the gene expression profiles of the mesenchymal and epithelial compartments of the E13 mouse bladder neck/urethral compartment. FVB/N mice were time mated. At embryonic day 13 mice were euthanized by decapitation and the bladders were microdissected and cut just below the ureters. Since the EDTA dissociation was ineffective, the bladder neck and urethra were collected and treated with 1 mg/ml trypsin in Tyrode's solution for 20 minutes at 37°C. The layers were separated using a fine needle and rimming. The samples were placed in RLT and stored at -80°C. RNA was prepared and the Epicentre 2-round amplification scheme described under the Lessard Group Protocols on the GUDMAP pages were performed. The amplified RNA was examined with the Affymetrix GeneChip Mouse Genome 430 2.0 Array.
2009-04-24 | E-GEOD-15794 | biostudies-arrayexpress