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HcaR DNA-binding transcriptional dual regulator

Synonyms: HcaR-HCA, HcaR
Summary:
HcaR, "hydrocinnamic acid regulator," directly regulates genes involved in 3-phenylpropionate (also called hydrocinnamic acid) catabolism.¿¿Proteome analyses have shown that HcaR regulates the production of 30 proteins involved in several processes; however, it is unknown whether this regulation is direct or indirect [2]. HcaR, which belongs to the LysR family, shows a helix-turn-helix motif in the N-terminal domain and a multimerization motif in the C-terminal domain [1]. It is not currently known how many monomers form the multimeric complex. A putative HcaR DNA-binding site sequence of 13 bp, matching the binding motif of LysR-type regulators, has been identified [1]. Homologous proteins 100% identical to HcaR have been found in pathogenic Escherichia coli strains, including O157:H7, and in Shigella flexneri [2]. The hcaR gene, which is transcribed divergently from an HcaR-regulated operon, is induced during stationary phase in an RpoS-independent manner, whereas it is repressed in the presence of glucose [3]and in the absence of oxygen through the indirect effect of ArcA [2] Read more >


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
HcaR Functional   nd [1], [2]
HcaR-HCA Functional   [HIFS], [IEP] [1], [3]
Evolutionary Family: LysR
Connectivity class: Local Regulator
Gene name: hcaR
  Genome position: 2668006-2668896
  Length: 891 bp / 296 aa
Operon name: hcaR
TU(s) encoding the TF:
Transcription unit        Promoter
hcaR
hcaRp


Regulon       
Regulated gene(s) hcaB, hcaC, hcaD, hcaE, hcaF, hcaR
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
carbon compounds (6)
Transcription related (1)
activator (1)
repressor (1)
operon (1)
Regulated operon(s) hcaEFCBD, hcaR
First gene in the operon(s) hcaE, hcaR
Simple and complex regulons HcaR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[HcaR,+](1)
[HcaR,-](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
  HcaR-HCA activator hcaEp nd -42.0 -92.0 hcaE, hcaF, hcaC, hcaB, hcaD
tctcagctggTAGAAATTAACTAtttcacatat
2668934 2668946 [AIBSCS], [BPP], [GEA] [1], [2], [3]
  HcaR repressor hcaRp nd 25.0 -44.0 hcaR
atatgtgaaaTAGTTAATTTCTAccagctgaga
2668934 2668946 [AIBSCS], [BPP], [GEA] [1], [2], [3]


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


Evidence    

 [HIFS] Human inference of function from sequence

 [IEP] Inferred from expression pattern

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis



Reference(s)    

 [1] Diaz E., Ferrandez A., Garcia JL., 1998, Characterization of the hca cluster encoding the dioxygenolytic pathway for initial catabolism of 3-phenylpropionic acid in Escherichia coli K-12., J Bacteriol 180(11):2915-23

 [2] Turlin E., Sismeiro O., Le Caer JP., Labas V., Danchin A., Biville F., 2005, 3-phenylpropionate catabolism and the Escherichia coli oxidative stress response., Res Microbiol 156(3):312-21

 [3] Turlin E., Perrotte-piquemal M., Danchin A., Biville F., 2001, Regulation of the early steps of 3-phenylpropionate catabolism in Escherichia coli., J Mol Microbiol Biotechnol 3(1):127-33



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