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PyrR DNA-binding transcriptional activator

Synonyms: PyrR-Pasp, PyrR, PyrR-BTS
Summary:
Based on genomic SELEX (gSELEX) screening, gel shift assay, and reporter assay, it was determined that PyrR is a dual regulator that acts as an activator for yhjX and yhcC and as a repressor for six other targets (pbpC, yfjD, gltBC, yghW, astCADBE, and xthA) [2]. There is unique cross-talk between low-affinity PyrSR and high-affinity BtsSR, which control the same exometabolite (pyruvate) but different sets of targets for pyruvate uptake and reutilization [2]. A mutant with deletion of both ypdA and ypdB does not show a significant phenotype when measured by phenotype microarray [3]. While wild-type E. coli shows significantly decreased swarming motility upon exposure to volatile organic compounds (VOCs) produced by Bacillus subtilis, a ypdB null mutant showed no significant difference in swarming motility upon VOC treatment []. PyrR: pyruvate reutilization regulator [2] Read more >


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
PyrR Non-Functional   Apo nd nd
PyrR-BTS Functional   Holo nd nd
PyrR-Pasp Functional   nd nd
Sensing class: External-Two-component systems
Connectivity class: Local Regulator
Gene name: pyrR
  Genome position: 2500383-2501117
  Length: 735 bp / 244 aa
Operon name: pyrSR-ypdC
TU(s) encoding the TF:
Transcription unit        Promoter
 
 


Regulon       
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 PyrR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[PyrR,+](1)


Transcription factor regulation    


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
  PyrR-BTS activator yhjXp Sigma70 -73.5 -109.5 yhjX
tcctgaactaAGGCATTTCATtccgttctga
3712112 3712122 [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/GS)], [CV(GEA/GS)], [CV(GEA/SM)], [CV(GEA/SM/GS)], [CV(SM)], [GEA], [GS], [SM] [1], [2]
  PyrR-BTS activator yhjXp Sigma70 -52.5 -88.5 yhjX
tccgttctgaTGGCATTTCATgccgtttttc
3712091 3712101 [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/GS)], [CV(GEA/GS)], [CV(GEA/SM)], [CV(GEA/SM/GS)], [CV(SM)], [GEA], [GS], [SM] [1], [2]


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


Evidence    

 [BPP] Binding of purified proteins

 [CV(GEA)] cross validation(GEA)

 [CV(GEA/GS)] cross validation(GEA/GS)

 [CV(GEA/SM)] cross validation(GEA/SM)

 [CV(GEA/SM/GS)] cross validation(GEA/SM/GS)

 [CV(SM)] cross validation(SM)

 [GEA] Gene expression analysis

 [GS] genomic SELEX

 [SM] Site mutation



Reference(s)    

 [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] Miyake Y., Inaba T., Watanabe H., Teramoto J., Yamamoto K., Ishihama A., 2019, Regulatory roles of pyruvate-sensing two-component system PyrSR (YpdAB) in Escherichia coli K-12., FEMS Microbiol Lett 366(2)

 [3] Zhou L., Lei XH., Bochner BR., Wanner BL., 2003, Phenotype microarray analysis of Escherichia coli K-12 mutants with deletions of all two-component systems., J Bacteriol 185(16):4956-72



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