Dissecting the PhoP regulatory network of Escherichia coli and Salmonella enterica.
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.
Zwir
Igor
I
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.
Shin
Dongwoo
D
Kato
Akinori
A
Nishino
Kunihiko
K
Latifi
Tammy
T
Solomon
Felix
F
Hare
Janelle M
JM
Huang
Henry
H
Groisman
Eduardo A
EA
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
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