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YpdB DNA-binding transcriptional activator

Synonyms: YpdB-phosphorylated
YpdB belongs to the LytTR response regulator (RR) of the two-component system [2]that participates in the carbon control network and may participate in nutrient scavenging before entry into stationary phase [1] It is composed of an N-terminal CheY-like receiver domain and a C-terminal LytTR-like effector domain with DNA-binding affinity [1] Chromatography analysis showed that YpdB is present as a monomeric form in solution [3]
A mimic of the phosphorylated form of YpdB has a higher capacity for binding to DNA compared to its unphosphorylated form [3]
YpdB binds to two direct repeats of the motif GGCATTTCAT, separated by an 11-bp spacer, in the yhjX promoter [1] 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 YpdB molecule to the lower-affinity site, and together they probably enhance the protein-DNA interactions [3]
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 [1]
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 [4] 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) [4]
YpdB is required for biofilm formation, and it is induced by VOCs [4, 5]
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 [4]

The YpdA/YpdB two-component system is widespread among proteobacteria and show a high degree of conservation in gammaproteobacteria [6]
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 [7] YpdA/YpdB is activated during growth in an amino acid-rich milieu, such as LB medium.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
YpdB-phosphorylated     nd nd
Sensing class: External-Two-component systems
Connectivity class: Local Regulator
Gene name: ypdB
  Genome position: 2500383-2501117
  Length: 735 bp / 244 aa
Operon name: ypdABC
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s) yhjX
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
Porters (Uni-, Sym- and Antiporters) (1)
membrane (1)
Regulated operon(s) yhjX
First gene in the operon(s) yhjX
Simple and complex regulons YpdB
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)

Transcription factor binding sites (TFBSs) arrangements       

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  YpdB-phosphorylated activator yhjXp Sigma70 -73.5 -109.5 yhjX
3712112 3712121 [BPP], [SM] [1]
  YpdB-phosphorylated activator yhjXp Sigma70 -52.5 -88.5 yhjX
3712091 3712100 [BPP], [SM] [1]

Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
Promoter-target gene evolutionary conservation


 [BPP] Binding of purified proteins

 [SM] Site mutation


 [1] Fried L., Behr S., Jung K., 2013, Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli., J Bacteriol. 195(4):807-15

 [2] Nikolskaya AN., Galperin MY., 2002, A novel type of conserved DNA-binding domain in the transcriptional regulators of the AlgR/AgrA/LytR family., Nucleic Acids Res. 30(11):2453-9

 [3] Behr S., Heermann R., Jung K., 2016, Insights into the DNA-binding mechanism of a LytTR-type transcription regulator., Biosci Rep. 36(2)

 [4] Kim KS., Lee S., Ryu CM., 2013, Interspecific bacterial sensing through airborne signals modulates locomotion and drug resistance., Nat Commun. 4:1809

 [5] Ren D., Zuo R., Gonzalez Barrios AF., Bedzyk LA., Eldridge GR., Pasmore ME., Wood TK., 2005, Differential gene expression for investigation of Escherichia coli biofilm inhibition by plant extract ursolic acid., Appl Environ Microbiol. 71(7):4022-34

 [6] Franceschini A., Szklarczyk D., Frankild S., Kuhn M., Simonovic M., Roth A., Lin J., Minguez P., Bork P., von Mering C., Jensen LJ., 2013, STRING v9.1: protein-protein interaction networks, with increased coverage and integration., Nucleic Acids Res. 41(Database issue):D808-15

 [7] Behr S., Fried L., Jung K., 2014, Identification of a Novel Nutrient-Sensing Histidine Kinase/Response Regulator Network in Escherichia coli., J Bacteriol. 196(11):2023-9