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.

Identification of a Novel Nutrient-Sensing Histidine Kinase/Response Regulator Network in Escherichia coli

“…The YehU/YehT and YpdA/YpdB systems are both known to be activated when E. coli is grown in an amino acid-rich milieu, such as LB medium. Furthermore, we had previously shown, using promoter luciferase activity assays, that expression of yjiY and yhjX begins at the onset of the transition into stationary phase (3). In this study, we quantitatively analyzed the levels of yjiY and yhjX mRNAs in a growing culture over time.…”

“…In addition, YehU and YpdA each possess a GAF domain, which is potentially capable of binding cyclic GMP, proteins, or ions (7,8), although its function remains unclear in most of the proteins in which it is found (9). The YehU/YehT system is activated in response to the presence of peptides or amino acids (2), while the available evidence suggests that the stimulus sensed by YpdA is pyruvate (3).…”

“…E scherichia coli contains 30 histidine kinases (HKs) and 32 response regulators (RRs) (1), some of which are still not very well understood. The YehU/YehT and YpdA/YpdB systems have recently been characterized in more detail in our laboratory (2,3). Both HKs and RRs are over 30% identical at the amino acid sequence level and share the same pattern of structural domains (4,5).…”

“…Under activating conditions, YehT induces yjiY, which codes for a transporter belonging to the CstA superfamily (2). YpdB regulates the expression of yhjX, which encodes a transporter of unknown function belonging to the major facilitator superfamily (3).…”

The hierarchic network of metal-response transcription factors in Escherichia coli

“…109) In addition, all TCS of E. coli K-12 have been characterized by the efforts to analyze unidentified response regulators, CitA-CitB, 110,111) CreCCreB, 112) GlrK/QseE-GlrR/QseF, 113,114) QseC-QseB, 105) RstB-RstA, 102) YehU-YehT, 115) and YpdA-YpdB. 116) This represents the signal transduction system of all TCSs of E. coli K-12, which are classified into three groups by regulatory functions.…”