title: Identification of a target gene and activating stimulus for the YpdA/YpdB histidine kinase/response regulator system in Escherichia coli.
abstract: Escherichia coli contains 30 two-component systems (TCSs), each consisting of a histidine kinase and a response regulator. Whereas most TCSs are well characterized in this model organism, little is known about the YpdA/YpdB system. To identify YpdB-regulated genes, we compared the transcriptomes of E. coli cells overproducing either YpdB or a control protein. Expression levels of 15 genes differed by more than 1.9-fold between the two strains. A comprehensive evaluation of these genes identified yhjX as the sole target of YpdB. Electrophoretic mobility shift assays with purified YpdB confirmed its interaction with the yhjX promoter. Specifically, YpdB binds to two direct repeats of the motif GGCATTTCAT separated by an 11-bp spacer in the yhjX promoter. yhjX encodes a cytoplasmic membrane protein of unknown function that belongs to the major facilitator superfamily of transporters. Finally, we characterized the pattern of yhjX expression and identified extracellular pyruvate as a stimulus for the YpdA/YpdB system. It is suggested that YpdA/YpdB contributes to nutrient scavenging before entry into stationary phase.
authors.affiliation: Munich Center for Integrated Protein Science (CIPSM) at the Department of Microbiology, Ludwig-Maximilians Universität München, Martinsried, Germany.
authors.forename: Luitpold
authors.initials: L
authors.lastname: Fried
authors.forename: Stefan
authors.initials: S
authors.lastname: Behr
authors.forename: Kirsten
authors.initials: K
authors.lastname: Jung
mesh_terms: D001665:Binding Sites; D018983:DNA Footprinting; D004269:DNA, Bacterial / Q000235:genetics; D003850:Deoxyribonuclease I; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism*; D017353:Gene Deletion; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology*; D005838:Genotype; D000071677:Histidine Kinase; D026901:Membrane Transport Proteins / Q000235:genetics / Q000378:metabolism*; D010957:Plasmids / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D011485:Protein Binding; D011494:Protein Kinases / Q000235:genetics* / Q000378:metabolism*; D011773:Pyruvates / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D001616:beta-Galactosidase
chemical_list: D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D026901:Membrane Transport Proteins; D011773:Pyruvates; D014157:Transcription Factors; C579564:YhjX protein, E coli; C579563:YpdB protein, E coli; D011494:Protein Kinases; D000071677:Histidine Kinase; C579562:YpdA protein, E coli; D003850:Deoxyribonuclease I; D001616:beta-Galactosidase