Abstract
Microbes can tailor transcriptional responses to diverse environmental challenges despite having streamlined genomes and a limited number of regulators. Here, we present data-driven models that capture the dynamic interplay of the environment and genome-encoded regulatory programs of two types of prokaryotes: Escherichia coli (a bacterium) and Halobacterium salinarum (an archaeon). The models reveal how the genome-wide distributions of cis-acting gene regulatory elements and the conditional influences of transcription factors at each of those elements encode programs for eliciting a wide array of environment-specific responses. We demonstrate how these programs partition transcriptional regulation of genes within regulons and operons to re-organize gene-gene functional associations in each environment. The models capture fitness-relevant co-regulation by different transcriptional control mechanisms acting across the entire genome, to define a generalized, system-level organizing principle for prokaryotic gene regulatory networks that goes well beyond existing paradigms of gene regulation. An online resource (http://egrin2.systemsbiology.net) has been developed to facilitate multiscale exploration of conditional gene regulation in the two prokaryotes.
Original language | English (US) |
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Article number | 740 |
Journal | Molecular Systems Biology |
Volume | 10 |
Issue number | 7 |
DOIs | |
State | Published - Jul 2014 |
Externally published | Yes |
Keywords
- EGRIN
- gene regulatory networks
- systems biology
- transcriptional regulation
ASJC Scopus subject areas
- General Agricultural and Biological Sciences
- Information Systems
- Applied Mathematics
- General Biochemistry, Genetics and Molecular Biology
- General Immunology and Microbiology
- Computational Theory and Mathematics