Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains
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ABSTRACT:
ORGANISM(S): Escherichia coli K-12 Escherichia coli
PROVIDER: GSE7398 | GEO | 2007/08/15
SECONDARY ACCESSION(S): PRJNA97889
REPOSITORIES: GEO
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series:; GSE7379: Fis KO strain; GSE7380: WT (Fis+) strain Experiment Overall Design: Refer to individual Series
2008-06-15 | E-GEOD-7398 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below.
2011-01-15 | GSE24572 | GEO
Project description:BackgroundIn addition to carbapenemases, dissemination of recently reported Escherichia coli lineages possessing a four amino acid insertion in PBP3 (encoded by ftsI) that confers reduced susceptibility to PBP3-targeted β-lactams, such as ceftazidime, can pose a threat of antimicrobial resistance.ObjectivesTo evaluate genotypic and phenotypic characteristics of E. coli possessing the mutated PBP3 collected during SIDERO-WT-2014 surveillance.MethodsA subset of 65 E. coli clinical isolates with MICs ≥2 mg/L for ceftazidime/avibactam, ceftolozane/tazobactam or cefiderocol, among a total of 1529 isolates from the multinational surveillance study, were subjected to gene analysis and antimicrobial susceptibility testing. Isogenic PBP3 mutants were constructed to confirm experimentally an impact on antimicrobial susceptibility.ResultsEleven strains possessing a YRIN-inserted PBP3 were identified, consisting of nine strains collected from the same hospital in Turkey (ST1284) and one each from the USA and Italy (ST361). Strains associated with each ST lineage possessed similar genetic backgrounds including β-lactamase genotypes; all nine strains from Turkey carried CMY-42, OXA-1 and the OXA-181 carbapenemase (five strains additionally carried CTX-M-15 ESBL), whereas the two other strains carried CMY-42 and TEM-1, indicating dissemination driven by selective pressure. The presence of the YRIN insertion contributed to reduced susceptibility to aztreonam, ceftazidime, cefepime and ceftolozane/tazobactam, although the strains remained susceptible to ceftazidime/avibactam despite relatively high MICs.ConclusionsE. coli strains of both ST1284 and ST361 lineages, possessing YRIN-inserted PBP3, are disseminating in several regions. The YRIN insertion in PBP3 occurred with multiple β-lactamases, which indicates frequent cross-resistance to other β-lactams.
| S-EPMC8210206 | biostudies-literature
Project description:Fis is a nucleoid-associated protein in E. coli that is abundant during early logarithmic growth in rich medium but is in short supply during stationary phase. Its role as a transcriptional regulator has been demonstrated for an increasing number of genes. In order to gain insight into the global effects of Fis on E. coli gene expression during different stages of growth in rich medium, DNA microarray analyses were conducted in fis and wild type strains during early log, mid log, late log, and stationary growth phases. We used microarrays to detail the global impact of Fis on gene expression in Escherichia coli Keywords: time course
2007-08-15 | GSE7379 | GEO
Project description:Fis is a nucleoid-associated protein in E. coli that is abundant during early logarithmic growth in rich medium but is in short supply during stationary phase. Its role as a transcriptional regulator has been demonstrated for an increasing number of genes. In order to gain insight into the global effects of Fis on E. coli gene expression during different stages of growth in rich medium, DNA microarray analyses were conducted in fis and wild type strains during early log, mid log, late log, and stationary growth phases. We used microarrays to detail the global impact of Fis on gene expression in Escherichia coli Keywords: time course
2007-08-15 | GSE7380 | GEO
Project description:The intracellular concentration of the Escherichia coli factor for inversion stimulation (Fis), a global regulator of transcription and a facilitator of certain site-specific DNA recombination events, varies substantially in response to changes in the nutritional environment and growth phase. Under conditions of nutritional upshift, fis is transiently expressed at very high levels, whereas under induced starvation conditions, fis is repressed by stringent control. We show that both of these regulatory processes operate on the chromosomal fis genes of the enterobacteria Klebsiella pneumoniae, Serratia marcescens, Erwinia carotovora, and Proteus vulgaris, strongly suggesting that the physiological role of Fis is closely tied to its transcriptional regulation in response to the nutritional environment. These transcriptional regulatory processes were previously shown to involve a single promoter (fis P) preceding the fis operon in E. coli. Recent work challenged this notion by presenting evidence from primer extension assays which appeared to indicate that there are multiple promoters upstream of fis P that contribute significantly to the expression and regulation of fis in E. coli. Thus, a rigorous analysis of the fis promoter region was conducted to assess the contribution of such additional promoters. However, our data from primer extension analysis, S1 nuclease mapping, beta-galactosidase assays, and in vitro transcription analysis all indicate that fis P is the sole E. coli fis promoter in vivo and in vitro. We further show how certain conditions used in the primer extension reactions can generate artifacts resulting from secondary annealing events that are the likely source of incorrect assignment of additional fis promoters.
| S-EPMC303451 | biostudies-literature
Project description:We have performed ChIP-Seq experiment for the global regulators, CRP and Fis in early and mid exponential growth phases respectively in Escherichia coli K12 MG1655. The dataset contains the genome wide binding patterns of Fis and CRP in the wildtype and the mutant strains
2016-12-13 | GSE92255 | GEO
Project description:To quantify the transcription level of genes for Escherichia coli DY330 in different growth phases a series of RNA-Seq experiments was performed.
2022-01-01 | GSE181687 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE24415: Comparison of gene expression of L. reuteri ATCC PTA 6475 at different growth phase in a LDMIII GSE24570: Comparison of gene expression of L. reuteri ATCC 55730 at different growth phase in LDMIII medium Refer to individual Series
2011-01-15 | E-GEOD-24572 | biostudies-arrayexpress
Project description:The Escherichia coli protein Fis is remarkable for its ability to interact specifically with DNA sites of highly variable sequences. The mechanism of this sequence-flexible DNA recognition is not well understood. In a previous study, we examined the contributions of Fis residues to high-affinity binding at different DNA sequences using alanine-scanning mutagenesis and identified several key residues for Fis-DNA recognition. In this work, we investigated the contributions of the 15-bp core Fis binding sequence and its flanking regions to Fis-DNA interactions. Systematic base-pair replacements made in both half sites of a palindromic Fis binding sequence were examined for their effects on the relative Fis binding affinity. Missing contact assays were also used to examine the effects of base removal within the core binding site and its flanking regions on the Fis-DNA binding affinity. The results revealed that: (1) the -7G and +3Y bases in both DNA strands (relative to the central position of the core binding site) are major determinants for high-affinity binding; (2) the C(5) methyl group of thymine, when present at the +4 position, strongly hinders Fis binding; and (3) AT-rich sequences in the central and flanking DNA regions facilitate Fis-DNA interactions by altering the DNA structure and by increasing the local DNA flexibility. We infer that the degeneracy of specific Fis binding sites results from the numerous base-pair combinations that are possible at noncritical DNA positions (from -6 to -4, from -2 to +2, and from +4 to +6), with only moderate penalties on the binding affinity, the roughly similar contributions of -3A or G and +3T or C to the binding affinity, and the minimal requirement of three of the four critical base pairs to achieve considerably high binding affinities.
| S-EPMC2292415 | biostudies-literature