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Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states.
- Source :
-
BMC biology [BMC Biol] 2014 Jan 24; Vol. 12, pp. 4. Date of Electronic Publication: 2014 Jan 24. - Publication Year :
- 2014
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Abstract
- Background: At the beginning of the transcription process, the RNA polymerase (RNAP) core enzyme requires a σ-factor to recognize the genomic location at which the process initiates. Although the crucial role of σ-factors has long been appreciated and characterized for many individual promoters, we do not yet have a genome-scale assessment of their function.<br />Results: Using multiple genome-scale measurements, we elucidated the network of σ-factor and promoter interactions in Escherichia coli. The reconstructed network includes 4,724 σ-factor-specific promoters corresponding to transcription units (TUs), representing an increase of more than 300% over what has been previously reported. The reconstructed network was used to investigate competition between alternative σ-factors (the σ70 and σ38 regulons), confirming the competition model of σ substitution and negative regulation by alternative σ-factors. Comparison with σ-factor binding in Klebsiella pneumoniae showed that transcriptional regulation of conserved genes in closely related species is unexpectedly divergent.<br />Conclusions: The reconstructed network reveals the regulatory complexity of the promoter architecture in prokaryotic genomes, and opens a path to the direct determination of the systems biology of their transcriptional regulatory networks.
- Subjects :
- DNA-Directed RNA Polymerases metabolism
Databases, Genetic
Holoenzymes metabolism
Promoter Regions, Genetic
Protein Binding
Regulon genetics
Transcription Initiation Site
Transcription, Genetic
Escherichia coli genetics
Gene Regulatory Networks
Genome, Bacterial genetics
Sigma Factor chemistry
Sigma Factor metabolism
Subjects
Details
- Language :
- English
- ISSN :
- 1741-7007
- Volume :
- 12
- Database :
- MEDLINE
- Journal :
- BMC biology
- Publication Type :
- Academic Journal
- Accession number :
- 24461193
- Full Text :
- https://doi.org/10.1186/1741-7007-12-4