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, 9] 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, 9].
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, 9].
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 [1, 4, 5].
In the presence of l-rhamnose, RhaR binds in tandem to two repeat sequences upstream of the rhaS intergenic region to activate transcription by overlapping the -35 box of rhaSp. The binding targets for RhaR consist of 17-nucleotide-long sequences that possess conserved motifs; each monomer binds to one of these conserved sequences located on different faces of the DNA 
|Sensing class:||External sensing using transported metabolites|
|Connectivity class:||Local Regulator|
|Length:||849 bp / 282 aa|
|TU(s) encoding the TF:||
|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)
|First gene in the operon(s)||rhaS|
|Simple and complex regulons|
|Simple and complex regulatory phrases||
Regulatory phrase (List of promoters regulated by the phrase)
|Transcription factor regulation|
|Functional conformation||Function||Promoter||Sigma factor||Central Rel-Pos||Distance to first Gene||Genes||Sequence
||LeftPos||RightPos||Evidence (Confirmed, Strong, Weak)||References|
|4097629||4097645||[BCE], [BPP], [GEA], [HIBSCS]||, , , |
|4097663||4097679||[BPP], [GEA], [HIBSCS]||, , , , , |
|Evolutionary conservation of regulatory elements|
 Kolin A., Balasubramaniam V., Skredenske JM., Wickstrum JR., Egan SM., 2008, Differences in the mechanism of the allosteric l-rhamnose responses of the AraC/XylS family transcription activators RhaS and RhaR., Mol Microbiol. 68(2):448-61
 Wickstrum JR., Skredenske JM., Kolin A., Jin DJ., Fang J., Egan SM., 2007, Transcription activation by the DNA-binding domain of the AraC family protein RhaS in the absence of its effector-binding domain., J Bacteriol. 189(14):4984-93
 Wickstrum JR., Santangelo TJ., Egan SM., 2005, Cyclic AMP receptor protein and RhaR synergistically activate transcription from the L-rhamnose-responsive rhaSR promoter in Escherichia coli., J Bacteriol. 187(19):6708-18