Computation-Directed Identification of OxyR DNA Binding Sites in Escherichia coli
| Autor: | Ming Zheng, Bernard Doan, Thomas D. Schneider, Xunde Wang, Gisela Storz, Karen A. Lewis |
|---|---|
| Rok vydání: | 2001 |
| Předmět: |
DNA
Bacterial Transcriptional Activation Molecular Sequence Data Repressor Genetics and Molecular Biology Biology Microbiology Gene Expression Regulation Enzymologic Primer extension Bacterial Proteins Iron-Binding Proteins Escherichia coli Binding site Promoter Regions Genetic Molecular Biology Gene Transcription factor Binding Sites Base Sequence Escherichia coli Proteins DNase-I Footprinting Promoter Gene Expression Regulation Bacterial Peroxiredoxins Molecular biology DNA-Binding Proteins Repressor Proteins DNA binding site Peroxidases Periplasmic Binding Proteins bacteria Periplasmic Proteins Oxidoreductases Bacterial Outer Membrane Proteins Transcription Factors |
| Zdroj: | Journal of Bacteriology. 183:4571-4579 |
| ISSN: | 1098-5530 0021-9193 |
| DOI: | 10.1128/jb.183.15.4571-4579.2001 |
| Popis: | A computational search was carried out to identify additional targets for the Escherichia coli OxyR transcription factor. This approach predicted OxyR binding sites upstream of dsbG , encoding a periplasmic disulfide bond chaperone-isomerase; upstream of fhuF , encoding a protein required for iron uptake; and within yfdI . DNase I footprinting assays confirmed that oxidized OxyR bound to the predicted site centered 54 bp upstream of the dsbG gene and 238 bp upstream of a known OxyR binding site in the promoter region of the divergently transcribed ahpC gene. Although the new binding site was near dsbG , Northern blotting and primer extension assays showed that OxyR binding to the dsbG -proximal site led to the induction of a second ahpCF transcript, while OxyR binding to the ahpCF -proximal site leads to the induction of both dsbG and ahpC transcripts. Oxidized OxyR binding to the predicted site centered 40 bp upstream of the fhuF gene was confirmed by DNase I footprinting, but these assays further revealed a second higher-affinity site in the fhuF promoter. Interestingly, the two OxyR sites in the fhuF promoter overlapped with two regions bound by the Fur repressor. Expression analysis revealed that fhuF was repressed by hydrogen peroxide in an OxyR-dependent manner. Finally, DNase I footprinting experiments showed OxyR binding to the site predicted to be within the coding sequence of yfdI . These results demonstrate the versatile modes of regulation by OxyR and illustrate the need to learn more about the ensembles of binding sites and transcripts in the E. coli genome. |
| Databáze: | OpenAIRE |
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