YpdB belongs to the LytTR response regulator (RR) of the two-component system |CITS:| that participates in the carbon control network and may participate in nutrient scavenging before entry into stationary phase |CITS:|. It is composed of an N-terminal CheY-like receiver domain and a C-terminal LytTR-like effector domain with DNA-binding affinity |CITS:|. Chromatography analysis showed that YpdB is present as a monomeric form in solution |CITS:|.
A mimic of the phosphorylated form of YpdB has a higher capacity for binding to DNA compared to its unphosphorylated form |CITS:|.
YpdB binds to two direct repeats of the motif GGCATTTCAT, separated by an 11-bp spacer, in the yhjX promoter |CITS:|. The YpdB-binding sites in the yhjX promoter have different affinities; the YpdB-binding site, with its higher affinity, is important for the stability and for the binding of a second YpdN molecule to the lower-affinity site, and together they probably enhance the protein-DNA interactions |CITS:|.
Based on genome scanning and microarray analysis, it has been determined that yhjX is the sole target gene regulated by the YpdA/YpdB system, and it is modulated by the sequence-dependent structure of the surrounding DNA |CITS:|.
Based on microarray analyses of Escherichia coli, 2,3-butanedione (2,3-BD) and glyoxylic acid (GA), volatile organic compounds (VOCs) emitted from Bacillus subtilis, mediated global changes in gene expression related to motility and antibiotic resistance phenotypes that affected the expression of more than 100 genes |CITS:|.
These changes were mediated by YpdB through the regulation of the transcription factors SoxS, YjhU, and the RpoS sigma factor, which were increased by treatment with (2,3-BD) |CITS:|.Read more >
YpdB is required for biofilm formation, and it is induced by VOCs |CITS:|.
The expression of hipA was severely reduced in the ypdB knockout, which suggests that the ypdB gene product might function as an upstream activator or transcription factor for hipA expression |CITS:|.
The YpdA/YpdB two-component system is widespread among proteobacteria and show a high degree of conservation in gammaproteobacteria |CITS:|.
The YpdA/YpdB system stimulates expression of the yjiY gene, the target of the YehU/YehT system, which suggests an interconnectivity between the two systems |CITS:|. YpdA/YpdB is activated during growth in an amino acid-rich milieu, such as LB medium. It responds to extracellular pyruvate |CITS:|.
YehU/YehT and YpdA/YpdB two-component systems are activated and expression of the corresponding target genes was found to occur at the same time as the onset of the stationary phase |CITS:|.
In vivo studies detected crosswise stimulus-dependent alterations in the expression of their respective target genes, and mutational analyses revealed that deletion of any of the components of the signal transduction cascade affects the function of the other. On the other hand, in vivo protein-protein interaction assays suggested that both systems together form a single large signaling unit |CITS:|.
Activation of the YehU/YehT signaling cascade, which results in YjiY production, suppresses YpdA/YpdB-mediated yhjX induction, whereas activation of the YpdA/YpdB signaling cascade, as well as inducing the synthesis of YhjX, promotes expression of yjiY |CITS:|.
|Sensing class:||External-Two-component systems|
|Connectivity class:||Local Regulator|
|Length:||735 bp / 244 aa|
|TU(s) encoding the TF:||
|Multifun term(s) of regulated gene(s)||
MultiFun Term (List of genes associated to the multifun term)
Porters (Uni-, Sym- and Antiporters) (1)
|First gene in the operon(s)||yhjX|
|Simple and complex regulons|
|Simple and complex regulatory phrases||
Regulatory phrase (List of promoters regulated by the phrase)
|Functional conformation||Function||Promoter||Sigma factor||Central Rel-Pos||Distance to first Gene||Genes||Sequence||LeftPos||RightPos||Evidence (Confirmed, Strong, Weak)||References|
|Evolutionary conservation of regulatory elements|