| Title | Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states. |
| Year of Publication | 2014 |
| Authors | B.K. Cho; D. Kim; E.M. Knight; K. Zengler; B.O. Palsson |
| Journal | PLoS Comput Biol |
| 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. |
| URL | http://www.ncbi.nlm.nih.gov/pubmed/24461193?dopt=Abstract |
| PubMed ID | 24461193 |
