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Open Access Research article

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

Byung-Kwan Cho12, Donghyuk Kim1, Eric M Knight1, Karsten Zengler1 and Bernhard O Palsson13*

  • * Corresponding author: Bernhard O Palsson palsson@ucsd.edu

  • † Equal contributors

Author Affiliations

1 Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA

2 Current address: Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-751, Republic of Korea

3 Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark

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BMC Biology 2014, 12:4  doi:10.1186/1741-7007-12-4

Published: 24 January 2014

Additional files

Additional file 1: Figure S1:

Strand specificity of RNA polymerase (RNAP) binding. Figure S2. Sequence motifs of σ-factors. Figure S3. The majority of σ38-specific promoters were bound by σ70 when rpoS is missing. Figure S4. Examples of up-regulated and down-regulated genes when rpoS was knocked out. Figure S5. Comparison of transcriptional regulation by two major σ-factors, σ70 and σ38, in two closely related bacteria. Figure S6. Comparison of transcriptional level of σ-factors and their anti-σ-factors. Figure S7. Purine and pyrimidine preferences at transcription start site (TSS) and −1 site. Figure S8. Number of TSSs found in one or multiple conditions. Figure S9. Clusters of Orthologous Groups (COG) clustering analysis of σ-factor regulons.

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Additional file 2: Table S1:

Escherichia coli strains and culture conditions for chromatin immunoprecipitation and microarray (ChIP-chip) experiments.

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Additional file 3: Table S2:

RRNA polymerase (RNAP) and σ-factor binding regions in Escherichia coli.

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Additional file 4: Table S3:

Binding intensities of RNA polymerase (RNAP) and σ-factor binding regions.

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Additional file 5: Table S5:

Comparison of σ-factor binding regions with known binding regions.

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Additional file 6: Table S4:

Identified TSSs of Escherichia coli under four different conditions.

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Additional file 7: Table S6:

Reconstructed σ-factor-transcription unit gene (σ-TUG) network in Escherichia coli.

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Additional file 8: Table S7:

Transcription levels of Escherichia coli genes in the wild type and the ΔrpoS strain.

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