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RhaR DNA-binding transcriptional activator

Synonyms: RhaR-L-rhamnose, RhaR-α-L-rhamnopyranose, RhaR
The "Rhamnose regulator," RhaR, is a transcription factor that regulates genes involved in L-rhamnose degradation and coregulates with the global transcriptional regulator CRP. These regulators bind cooperatively to activate transcription of the unusual operon rhaSR, which encodes two transcriptional regulators, RhaS and RhaR (30% identical), both members of the AraC/XylS family of transcriptional regulators and involved in L-rhamnose transport and degradation [3, 4]. In vitro transcription assays indicate that the α-CTD of the RNA polymerase is partially dispensable for RhaR activation and is required for CRP activation of the rhaSR operon [3, 4]. Apparently, expression of the operons involved in transport and degradation of L-rhamnose first requires expression of RhaR, which induces transcription of the rhaSR operon. In this way, RhaS activates transcription of L-rhamnose gene clusters. Transcription of the rhaSR operon is induced when E. coli is grown on L-rhamnose in the absence of glucose. Gene induction occurs when the physiological inducer, L-rhamnose, binds to RhaR and when cellular cyclic AMP levels are high [3, 4]. This transcription factor is composed of two domains, a C-terminal domain that contains two potential helix-turn-helix DNA-binding motifs and an N-terminal domain involved in l-rhamnose binding and dimerization of the protein [2, 5, 6].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
RhaR Non-Functional   Apo nd nd
RhaR-α-L-rhamnopyranose Functional Allosteric Holo nd nd
RhaR-L-rhamnose Functional   Holo [APPH], [HIFS], [IEP] [1], [2]
Evolutionary Family: AraC/XylS
Sensing class: External sensing using transported metabolites
Connectivity class: Local Regulator
Gene name: rhaR
  Genome position: 4098646-4099494
  Length: 849 bp / 282 aa
Operon name: rhaSR
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s) rhaR, rhaS
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
carbon compounds (2)
Transcription related (2)
activator (2)
operon (2)
Regulated operon(s) rhaSR
First gene in the operon(s) rhaS
Simple and complex regulons CRP,RhaR,RhaS
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)

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
  RhaR-L-rhamnose activator rhaSp Sigma70 -74.0 -99.0 rhaS, rhaR
4097629 4097645 [BPP], [GEA] [2]
  RhaR-L-rhamnose activator rhaSp Sigma70 -40.0 -65.0 rhaS, rhaR
4097663 4097679 [APIORCISFBSCS], [BPP], [GEA] [2]
  RhaR-L-rhamnose activator rhaSp2 Sigma38 -74.0 -99.0 rhaS, rhaR
4097629 4097645 [BPP], [GEA] [2]
  RhaR-L-rhamnose activator rhaSp2 Sigma38 -40.0 -65.0 rhaS, rhaR
4097663 4097679 [APIORCISFBSCS], [BPP], [GEA] [2]

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