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Issue 12, 2009
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Inferring the transcriptional network of Bacillus subtilis

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Abstract

The adaptation of bacteria to the vigorous environmental changes they undergo is crucial to their survival. They achieve this adaptation partly via intricate regulation of the transcription of their genes. In this study, we infer the transcriptional network of the Gram-positive model organism, Bacillus subtilis. We use a data integration workflow, exploiting both motif and expression data, towards the generation of condition-dependent transcriptional modules. In building the motif data, we rely on both known and predicted information. Known motifs were derived from DBTBS, while predicted motifs were generated by a de novo motif detection method that utilizes comparative genomics. The expression data consists of a compendium of microarrays across different platforms. Our results indicate that a considerable part of the B. subtilis network is yet undiscovered; we could predict 417 new regulatory interactions for known regulators and 453 interactions for yet uncharacterized regulators. The regulators in our network showed a preference for regulating modules in certain environmental conditions. Also, substantial condition-dependent intra-operonic regulation seems to take place. Global regulators seem to require functional flexibility to attain their roles by acting as both activators and repressors.

Graphical abstract: Inferring the transcriptional network of Bacillus subtilis

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Publication details

The article was received on 09 Apr 2009, accepted on 25 Jun 2009 and first published on 28 Jul 2009


Article type: Paper
DOI: 10.1039/B907310H
Mol. BioSyst., 2009,5, 1840-1852

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    Inferring the transcriptional network of Bacillus subtilis

    A. Fadda, A. C. Fierro, K. Lemmens, P. Monsieurs, K. Engelen and K. Marchal, Mol. BioSyst., 2009, 5, 1840
    DOI: 10.1039/B907310H

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