Project description:This SuperSeries is composed of the following subset Series:; GSE15404: Expression data from E. coli cells overexpressing GraL for short periods of time; GSE15405: Expression data from E. coli cells overexpressing GraL for long periods of time Experiment Overall Design: Refer to individual Series
Project description:Our laboratory has recently discovered that E. coli cells starved for the DNA precursor dGTP are killed efficiently (dGTP starvation) in a manner similar to that described for Thymineless Death (TLD). Conditions for specific dGTP starvation can be achieved by depriving an E. coli optA1 gpt strain of the purine nucleotide precursor hypoxanthine (Hx). To gain insight into the mechanisms underlying dGTP starvation, we conducted genome-wide gene expression analyses on actively growing optA1 gpt strains subjected to hypoxanthine deprivation for increasing periods of time. The data show that, upon Hx withdrawal, the optA1 gpt strain displays a diminished ability to de-repress the de novo purine biosynthesis genes, and this is likely due to internal guanine accumulation. The impairment to fully induce the purR regulon may be a contributing factor to the lethality of dGTP starvation. At later time points, and coinciding with cell lethality, strong induction of the SOS is observed, supporting the concept of replication stress as a final cause of death. No evidence was observed for the participation of other stress responses, including the rpoS-mediated global stress response in the starved cells, and reinforcing the lack of feedback of replication stress into the global metabolism of the cell. The genome-wide expression data also provide direct evidence for increased genome complexity during dGTP starvation, as a markedly increased gradient is observed for expression of genes located nearby the replication origin relative to those located towards the replication terminus.
Project description:Expression profiles of wild-type and SgrR mutant E. coli strains under aMG and 2-DG-induced stress. Expression profiles of E. coli overexpressing SgrS sRNA.
Project description:Expression profiles of wild-type and SgrR mutant E. coli strains under aMG and 2-DG-induced stress. Expression profiles of E. coli overexpressing SgrS sRNA. Illumina RNA-Seq of total RNA extracted from wild-type, SgrR/SgrS mutant and SgrS overexpressing E. coli strains grown in different conditions.
Project description:We uncovered evidence for an expanded role of transcription-coupled repair factor Mfd in Escherichia coli. In mfd knockout cells, expression of 75 genes was significantly increased while that of 18 genes was diminished. GO term analysis revealed that the affected genes were disproportionately from certain functional groups. RNA levels in the knockout deviated from wild type beginning at transcription start sites, arguing against premature termination as the cause. RNA-seq analysis in cells overexpressing Mfd revealed dramatic deviation of gene expression in the chromosome terminus region. Taken together, our data support a novel role for Mfd in transcription regulation.
Project description:The goal of this study is to compare gene expression data for a well known model organism (Escherichia coli) using different technologies (NGS here, microarray from GSE48776).
Project description:The purpose of this study is to determine whether the presence of pathogenic Escherichia coli in colon is associated with psychiatric disorders.
