Escherichia coli
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA667580 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12779500_1.fastq.gz | Fastqsanger.gz | |||
| SRR12779500_2.fastq.gz | Fastqsanger.gz | |||
| SRR12779501_1.fastq.gz | Fastqsanger.gz | |||
| SRR12779501_2.fastq.gz | Fastqsanger.gz | |||
| SRR12779502_1.fastq.gz | Fastqsanger.gz |
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Project description:Escherichia coli ESBL plasmid sequencing
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Project description:Transcription profiles in BL21, BL21/pOri1 and BL21/pOri2 were analysed using DNA microarray technology. BL21, BL21/pOri1 or BL21/pOri2 strains were cultured at chemostat status and harvested after the cultivation arrived steady status. Keywords: Effects of plasmid DNA on Escherichia coli metabolism
2006-07-07 | GSE5239 | GEO
Project description:Background: It remains unclear how high-risk Escherichia coli lineages, like sequence type (ST) 131, initially adapt to carbapenem exposure in its progression to becoming carbapenem resistant. Methods: Carbapenem mutation frequency was measured in multiple subclades of extended-spectrum β-lactamase (ESBL) positive ST131 clinical isolates using a fluctuation assay followed by whole genome sequencing (WGS) characterization. Genomic, transcriptomic, and porin analyses of ST131 C2/H30Rx isolate, MB1860, under prolonged, increasing carbapenem exposure was performed using two distinct experimental evolutionary platforms to measure fast vs. slow adaptation. Results: All thirteen ESBL positive ST131 strains selected from a diverse (n=184) ST131 bacteremia cohort had detectable ertapenem (ETP) mutational frequencies with a statistically positive correlation between initial ESBL gene copy number and mutation frequency (r = 0.87, P<1e-5). WGS analysis of mutants showed initial response to ETP exposure resulted in significant increases in ESBL gene copy numbers or mutations in outer membrane porin (Omp) encoding genes in the absence of ESBL gene amplification with subclade specific adaptations. In both experimental evolutionary platforms, MB1860 responded to initial ETP exposure by increasing blaCTX-M-15 copy numbers via modular, insertion sequence 26 (IS26) mediated pseudocompound transposons (PCTns). Transposase activity driven by PCTn upregulation was a conserved expression signal in both experimental evolutionary platforms. Stable mutations in Omp encoding genes were detected only after prolonged increasing carbapenem exposure consistent with clinical observations. Conclusions: ESBL gene amplification is a conserved response to initial carbapenem exposure, especially within the high-risk ST131 C2 subclade. Targeting such amplification could assist with mitigating carbapenem resistance development.
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Project description:IrrE is a unique gene in Deinococcus, which is the switch of DNA repair and celluar surival network. Expressing IrrE enhanced the salt tolence in E. coli. To understand the effect of IrrE to E. coli during salt shock, we constructed the IrrE-expressing plasmid pMG1-IrrE. And pMG1 is the empty vector used as a control. The GroESL promoter was amplified from D. radiodurans R1 genomic DNA by PCR with proper primers. The PCR product was ligated into the T-cloning site of T-vector pMD18T, generating the plasmid pMG1.
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Project description:In order to understand whether the evolutionary acquisition of virF gene may have altered the transcriptional program in Shigella's harmless ancestor (E. coli) promoting the inactivation of genes potetially detrimental to the full expression of the invasivity phenotype, we performed a global transcriptional analysis of E. coli cells expressing or lacking the virF gene. To this end we used the E. coli K12 MG1655 strain, carrying the virF-encoding plasmid pMYSH6504, or its virF depleted derivative pMY6504R.
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Project description:APEC most often infect chickens, turkeys, ducks, and other avian species, and therefore pose a significant economic burden on the poultry industry worldwide. Few studies have analyzed the genome-wide transcriptional profile of APEC during infection in vivo. In this study, we examined the genome-wide transcriptional response of APEC O2 strain E058 in an in vivo chicken infection model to better understand the factors necessary for APEC colonization, growth, and survival in vivo. An Affymetrix multigenome DNA microarray, which contains most of the genomic open reading frames of E. coli K-12 strain MG1655, uropathogenic E. coli strain CFT073, and E. coli O157:H7 strain EDL 933, was used to profile the gene expression in APEC E058.The genes highly expressed during infection were involved in metabolism, iron acquisition or transport, virulence, response to stress, and biological regulation. Many genes encoding putative or hypothetical proteins were also strongly upregulated, implying that some undiscovered mechanism may underlie APEC pathogenesis.
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Project description:Our study aimed to analyse the responses of the clonal ST131 strain, containing the ESBL and multi-drug resistance plasmid under different beta-lactam and ciprofloxacin antibiotic stress in comparison with no antibiotic stresses in order to identify the specific response of a MDR plasmid to the specific antibiotic and the potential interaction between the plasmid and the host bacteria under different stresses. The aim was to understand how the plasmid and bacterial host proteins are influenced by the different antibiotic stresses. By analysing these factors systematically we aimed to identify the pathways and core or antibiotic specific responses of the bacteria. Using proteomics we provide an unbiased protein map of a pathogen with a MDR plasmid under antibiotic stress and compare it with the same bacteria in the absence of the stress.
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Project description:Transcriptional profiling of E. coli cells comparing control harboring the empty vector pRadGro (Ec-pR) with E. coli expressing the Deinococcus radiodurans response regulator DR1558 (Ec-1558) Expression of DR1558 conferred to multi-stress tolerance to E. coli.
2015-07-10 | GSE70688 | GEO
Project description:In order to understand whether the evolutionary acquisition of virF gene may have altered the transcriptional program in Shigella's harmless ancestor (E. coli) promoting the inactivation of genes potetially detrimental to the full expression of the invasivity phenotype, we performed a global transcriptional analysis of E. coli cells expressing or lacking the virF gene. To this end we used the E. coli K12 MG1655 strain, carrying the virF-encoding plasmid pMYSH6504, or its virF depleted derivative pMY6504R. Two condition experiment: the E. coli K12 MG1655 strain, carrying the virF-encoding plasmid pMYSH6504, and its virF depleted derivative pMY6504R. Two replicate for each condition
2011-06-25 | E-GEOD-30207 | biostudies-arrayexpress
Project description:We performed a high-throughput mapping of the 5’ end transcriptome of the pAA plasmid of the clinical Escherichia coli O104:H4 (E. coli O104:H4) isolate LB226692. We employed differential RNA-sequencing (dRNA-seq), a terminator exonuclease (TEX)-based RNA-seq approach allowing for the discrimination of primary and processed transcripts. This method has proven to be a powerful tool for the mapping of transcription start sites (TSS) and detection of non-coding RNAs (ncRNAs) in bacteria. We catalogued pAA-associated TSS and processing sites on a plasmid-wide scale and performed a detailed analysis of the primary transcriptome focusing on pAA virulence gene expression.
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