Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states.

TitleGenome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states.
Publication TypeJournal Article
Year of Publication2014
AuthorsCho B-K, Kim D, Knight EM, Zengler K, Palsson BO
JournalBMC Biol
Volume12
Issue1
Pagination4
PubMed Date2014 Jan 24
ISSN1741-7007
Abstract

BACKGROUND: At the beginning of the transcription process, the RNAP core enzyme requires a sigma-factor to recognize the genomic location where the process initiates. Although the critical role of sigma-factors has been long appreciated and characterized for many individual promoters, we do not yet have a genome-scale assessment of their function.
RESULTS: Using multiple genome-scale measurements we elucidated the network of sigma-factor-promoter interactions in Escherichia coli. The reconstructed network includes 4,724 sigma-factor-specific promoters corresponding to transcription units (TU), representing more than a 300% increase over what has been previously. The reconstructed network was used to investigate competition between alternative sigma-factors the sigma70 and sigma38 regulons, confirming the competition model of sigma substitution and a negative regulation by alternative sigma-factors. Comparison to sigma-factor binding in Klebsiella pneumoniae shows that transcriptional regulation of conserved genes in closely related species is surprisingly divergent.Conclusoins: The reconstructed network reveals 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.

Alternate JournalBMC Biol.
PubMed ID24461193
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