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

BMC Biology

Research Article

Donghyuk Kim¹  Karsten Zengler¹  Eric M Knight¹  Byung-Kwan Cho²  Bernhard O Palsson³ 

[1] Department of Bioengineering, University of California, San Diego, 92093, La Jolla, CA, USA;Department of Bioengineering, University of California, San Diego, 92093, La Jolla, CA, USA;Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 305-751, Daejeon, Republic of Korea;Department of Bioengineering, University of California, San Diego, 92093, La Jolla, CA, USA;Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark;

关键词: Escherichia coli;    Sigma factor;    Network reconstruction;    Comparative analysis;    Klebsiella pneumoniae;    Omics data;    Systems biology;   

DOI  :  10.1186/1741-7007-12-4

 received in 2014-01-03, accepted in 2014-01-14,  发布年份 2014

来源: Springer

【 摘 要 】

BackgroundAt 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.ResultsUsing 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.ConclusionsThe 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.

【 授权许可】

Unknown   
© Cho et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.