E. coli strain E24377A
Ontology highlight
ABSTRACT:
ORGANISM(S): Escherichia coli E24377A
SUBMITTER: Jason Sahl
PROVIDER: E-GEOD-31806 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
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Project description:ETEC is an important human pathogen. Although the mechanism of diarrhea is known in ETEC, the regulatory networks are less understood. This study was conducted to understand the global expression of ETEC isolate E24377A under different growth and environmental conditions. ETEC E24377A was grown in LB or LB+bile salts (3% w/v). For each condition, three biological replicates were combined into a single sample.
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Project description:Gene regulatory networks play an important role in coordinating biochemical fluxes through diverse metabolic pathways. The modulation of enzyme levels enables efficient utilization of limited resources as organisms dynamically acclimate to nutritional fluctuations in their environment. Here we have identified and characterized a novel nutrient-responsive transcription factor from the halophilic archaea, VNG1451C. In this experiment we used whole-genome microarray analysis in the VNG1451C deletion mutant vs. H. salinarum NRC-1 ura3 parent strain in defined medium during growth with and without glucose to show that the expression of many metabolic genes is perturbed in the VNG1451C deletion mutant in response to this sugar. Halobacterium salinarum NRC-1 (ATCC700922) ura3 parent and VNG1451C strains were grown in complete defined medium (CDM; 20 amino acids at concentrations defined by Shand and Perez, 1999. NaCl 250g/L, MgSO4 20 g/L, KCl 1 g/L, NaH2PO4 0.167mM, Biotin 0.02mM, Thiamin 0.015mM, Folic acid 0.0113 mM, MnSO4 0.01mM, FeSO4, 0.01mM, glucose added at 10% w/v where indicated in sample files) at 37ºC under full-spectrum white light. Biological replicate samples were removed throughout the growth curve at early log, mid log, and stationary phase to measure genome-wide transcription.
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Project description:Because iron toxicity and deficiency are equally life threatening, maintaining intracellular iron levels within a narrow optimal range is critical for nearly all known organisms. However, regulatory mechanisms that establish homeostasis are not well understood in organisms that dwell in environments at the extremes of pH, temperature, and salinity. Under conditions of limited iron, the extremophile Halobacterium salinarum, a salt-loving archaeon, mounts a specific response to scavenge iron for growth. We have identified and characterized the role of two transcription factors (TFs), Idr1 and Idr2, in regulating this important response. An integrated systems analysis of TF knockout gene expression profiles and genome-wide binding locations in the presence and absence of iron has revealed that these TFs operate collaboratively to maintain iron homeostasis. In the presence of iron, Idr1 and Idr2 bind near each other at 24 loci in the genome, where they are both required to repress some genes. In contrast, Idr1 and Idr2 are both necessary to activate other genes in a putative a feed forward loop. Even at loci bound independently, the two TFs target different genes with similar functions in iron homeostasis. We discuss conserved and unique features of the Idr1-Idr2 system in the context of similar systems in organisms from other domains of life. Data in this GEO archive are linked to the publication: Schmid AK, Pan M, Sharma K, Baliga NS.2011. Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon.Nucleic Acids Res.39(7):2519-33. The Δura3 parent, Δidr2 and Δidr1, and Δ idr1Δidr2 mutant strains were grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in CDM with all trace metals except iron. Cultures were split in half and FeSO4 was added to one half, while the other was continued under iron limitation. 8-mL samples were collected from each culture every 20 minutes for 60 minutes (see also experimental design, Supplementary Figure 1, Schmid et al., 2011). RNA from two biological replicate time courses were prepared, averages of these replicates are reported in the published study, whereas data from each replicate are reported here. The zero time point was harvested immediately before the addition of iron. Each Sample is based on two arrrays (one with dye-swap).
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