| Full text | |
| Author(s): |
Brooks, Aaron N.
[1, 2]
;
Reiss, David J.
[1]
;
Allard, Antoine
[3]
;
Wu, Wei-Ju
[1]
;
Salvanha, Diego M.
[4, 1]
;
Plaisier, Christopher L.
[1]
;
Chandrasekaran, Sriram
[1]
;
Pan, Min
[1]
;
Kaur, Amardeep
[1]
;
Baliga, Nitin S.
[5, 1, 2, 6, 7]
Total Authors: 10
|
| Affiliation: | [1] Inst Syst Biol, Seattle, WA 98109 - USA
[2] Univ Washington, Mol & Cellular Biol Program, Seattle, WA 98195 - USA
[3] Univ Laval, Dept Phys Genie Phys & Opt, Quebec City, PQ - Canada
[4] Univ Sao Paulo, Dept Comp & Math FFCLRP USP, LabPIB, BR-14049 Ribeirao Preto - Brazil
[5] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Berkeley, CA 94720 - USA
[6] Univ Washington, Dept Microbiol, Seattle, WA 98195 - USA
[7] Univ Washington, Dept Biol, Seattle, WA 98195 - USA
Total Affiliations: 7
|
| Document type: | Journal article |
| Source: | MOLECULAR SYSTEMS BIOLOGY; v. 10, n. 7 JUL 2014. |
| Web of Science Citations: | 28 |
| 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. (AU) | |
| FAPESP's process: | 11/08104-4 - Integration tools for SNP-array analysis in variomics |
| Grantee: | Diego Martinez Salvanha |
| Support Opportunities: | Scholarships in Brazil - Doctorate (Direct) |
| FAPESP's process: | 12/05392-1 - Enabling Gaggle Genome-Browser to variomics research |
| Grantee: | Diego Martinez Salvanha |
| Support Opportunities: | Scholarships abroad - Research Internship - Doctorate (Direct) |