title: Dissecting the PhoP regulatory network of Escherichia coli and Salmonella enterica.
abstract: Genetic and genomic approaches have been successfully used to assign genes to distinct regulatory networks. However, the present challenge of distinguishing differentially regulated genes within a network is particularly hard because members of a given network tend to have similar regulatory features. We have addressed this challenge by developing a method, termed Gene Promoter Scan, that discriminates coregulated promoters by simultaneously considering both multiple cis promoter features and gene expression. Here, we apply this method to probe the regulatory networks governed by the PhoP/PhoQ two-component system in the enteric bacteria Escherichia coli and Salmonella enterica. Our analysis uncovered members of the PhoP regulon and interactions with other regulatory systems that were not discovered in previous approaches. The predictions made by Gene Promoter Scan were experimentally validated to establish that the PhoP protein uses multiple mechanisms to control gene transcription, regulates acid resistance determinants, and is a central element in a highly connected network.
authors.affiliation: Department of Molecular Microbiology, Howard Hughes Medical Institute, Washington University School of Medicine, Campus Box 8230, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
authors.forename: Igor
authors.initials: I
authors.lastname: Zwir
authors.forename: Dongwoo
authors.initials: D
authors.lastname: Shin
authors.forename: Akinori
authors.initials: A
authors.lastname: Kato
authors.forename: Kunihiko
authors.initials: K
authors.lastname: Nishino
authors.forename: Tammy
authors.initials: T
authors.lastname: Latifi
authors.forename: Felix
authors.initials: F
authors.lastname: Solomon
authors.forename: Janelle M
authors.initials: JM
authors.lastname: Hare
authors.forename: Henry
authors.initials: H
authors.lastname: Huang
authors.forename: Eduardo A
authors.initials: EA
authors.lastname: Groisman
mesh_terms: D001426:Bacterial Proteins / Q000502:physiology*; D004926:Escherichia coli / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000502:physiology*; D006863:Hydrogen-Ion Concentration; D010744:Phosphoric Monoester Hydrolases / Q000235:genetics; D011401:Promoter Regions, Genetic; D019779:Salmonella enterica / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; C465562:PhoP protein, E coli; C079792:PhoQ protein, Bacteria; C061064:PhoP protein, Bacteria; D010744:Phosphoric Monoester Hydrolases; C024329:3-deoxy-manno-octulosonate-8-phosphatase