title: Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks.
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.
authors.affiliation: Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA.
authors.forename: Yu
authors.initials: Y
authors.lastname: Qiu
authors.forename: Harish
authors.initials: H
authors.lastname: Nagarajan
authors.forename: Mallory
authors.initials: M
authors.lastname: Embree
authors.forename: Wendy
authors.initials: W
authors.lastname: Shieu
authors.forename: Elisa
authors.initials: E
authors.lastname: Abate
authors.forename: Katy
authors.initials: K
authors.lastname: Juárez
authors.forename: Byung-Kwan
authors.initials: BK
authors.lastname: Cho
authors.forename: James G
authors.initials: JG
authors.lastname: Elkins
authors.forename: Kelly P
authors.initials: KP
authors.lastname: Nevin
authors.forename: Christian L
authors.initials: CL
authors.lastname: Barrett
authors.forename: Derek R
authors.initials: DR
authors.lastname: Lovley
authors.forename: Bernhard O
authors.initials: BO
authors.lastname: Palsson
authors.forename: Karsten
authors.initials: K
authors.lastname: Zengler
mesh_terms: D004734:Energy Metabolism / Q000235:genetics; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks / Q000235:genetics*; D005798:Genes, Bacterial / Q000235:genetics; D045302:Geobacter / Q000235:genetics* / Q000254:growth & development; D008954:Models, Biological; D018085:Regulon / Q000235:genetics; D012808:Sigma Factor / Q000378:metabolism*
chemical_list: D012808:Sigma Factor