Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks.
Nat Commun, 2013;4:1755.
Qiu Y[1], Nagarajan H, Embree M, Shieu W, Abate E, Juárez K, Cho BK, Elkins JG, Nevin KP, Barrett CL, Lovley DR, Palsson BO, Zengler K
Affiliations
PMID: 23612296DOI: 10.1038/ncomms2743
Impact factor: 17.694
Abstract
Bacteria contain multiple sigma factors, each targeting diverse, but often overlapping sets of promoters, thereby forming a complex network. The layout and deployment of such a sigma factor network directly impacts global transcriptional regulation and ultimately dictates the phenotype. Here we integrate multi-omic data sets to determine the topology, the operational, and functional states of the sigma factor network in Geobacter sulfurreducens, revealing a unique network topology of interacting sigma factors. Analysis of the operational state of the sigma factor network shows a highly modular structure with σ(N) being the major regulator of energy metabolism. Surprisingly, the functional state of the network during the two most divergent growth conditions is nearly static, with sigma factor binding profiles almost invariant to environmental stimuli. This first comprehensive elucidation of the interplay between different levels of the sigma factor network organization is fundamental to characterize transcriptional regulatory mechanisms in bacteria.
MeSH terms
Energy Metabolism; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Gene Regulatory Networks; Genes, Bacterial; Geobacter; Models, Biological; Regulon; Sigma Factor
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