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BMC Biol. 2014 Jan 24;12:4. doi: 10.1186/1741-7007-12-4.

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

Author information

1
Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA. palsson@ucsd.edu.

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.

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.

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.

PMID:
24461193
PMCID:
PMC3923258
DOI:
10.1186/1741-7007-12-4
[Indexed for MEDLINE]
Free PMC Article
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