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RcnR DNA-binding transcriptional repressor

Synonyms: RcnR, RcnR-Co2+, RcnR-Ni 2+
The RcnR, resistance to cobalt and nickel regulator protein is an addition to the set of transcriptional metallo-regulator proteins of E. coli (some of the main ones are Fur, CueR, CusR, MntR, Zur, ZntR, and NikR) [2] that regulate the transcriptional expression of a recently described efflux protein, RcnA [6] to maintain nickel and cobalt homeostasis [2, 3] The homeostasis of different metals in the cell is constantly monitored, and adequate pathways are activated or repressed to keep the metals within normal levels. Specifically, when nickel and cobalt exceed the normal levels, cell growth stops [2]
The rcnR gene is encoded divergently to the rcnA gene, which encodes an efflux protein that is involved in nickel and cobalt homeostasis [6] it removes an excess of ions [2] It has been proved by Koch and colleagues [3]that the rcnR gene is the target of Fur regulation in regard to iron levels (when iron increases, rcnR expression increases about 2.3-fold [3].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
RcnR Functional   Apo [BPP], [GEA], [IPI] [1], [2], [3]
RcnR-Co2+ Non-Functional Allosteric Holo [BPP], [GEA], [IPI] [1], [2], [3]
RcnR-Ni 2+ Non-Functional Allosteric Holo [BPP], [GEA], [IPI] [1], [2], [3]
Evolutionary Family: RcnR_FrmR_like_DUF156
Connectivity class: Local Regulator
Gene name: rcnR
  Genome position: 2185524-2185796
  Length: 273 bp / 90 aa
Operon name: rcnR
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s) rcnA, rcnB, rcnR
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
Transporters of Unknown Classification (1)
membrane (1)
operon (1)
detoxification (1)
repressor (1)
Regulated operon(s) rcnAB, rcnR
First gene in the operon(s) rcnA, rcnR
Simple and complex regulons Fur,RcnR
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
  RcnR repressor rcnAp Sigma70 26.5 -65.0 rcnA, rcnB
2185845 2185859 [BPP], [GEA] [2], [3], [4], [5]
  RcnR repressor rcnAp Sigma70 46.5 -45.0 rcnA, rcnB
2185865 2185879 [BPP], [GEA] [2], [3], [4], [5]
  RcnR repressor rcnRp Sigma70 31.5 -76.0 rcnR
2185865 2185879 [BPP], [GEA] [2], [3], [4], [5]
  RcnR repressor rcnRp Sigma70 51.5 -56.0 rcnR
2185845 2185859 [BPP], [GEA] [2], [3], [4], [5]

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

 [GEA] Gene expression analysis

 [IPI] Inferred from physical interaction


 [1] Iwig JS., Leitch S., Herbst RW., Maroney MJ., Chivers PT., 2008, Ni(II) and Co(II) sensing by Escherichia coli RcnR., J Am Chem Soc. 130(24):7592-606

 [2] Iwig JS., Rowe JL., Chivers PT., 2006, Nickel homeostasis in Escherichia coli - the rcnR-rcnA efflux pathway and its linkage to NikR function., Mol Microbiol. 62(1):252-62

 [3] Koch D., Nies DH., Grass G., 2007, The RcnRA (YohLM) system of Escherichia coli: A connection between nickel, cobalt and iron homeostasis., Biometals. 20(5):759-71

 [4] Blaha D., Arous S., Bleriot C., Dorel C., Mandrand-Berthelot MA., Rodrigue A., 2010, The Escherichia coli metallo-regulator RcnR represses rcnA and rcnR transcription through binding on a shared operator site: Insights into regulatory specificity towards nickel and cobalt., Biochimie

 [5] Iwig JS., Chivers PT., 2009, DNA recognition and wrapping by Escherichia coli RcnR., J Mol Biol. 393(2):514-26

 [6] Rodrigue A., Effantin G., Mandrand-Berthelot MA., 2005, Identification of rcnA (yohM), a nickel and cobalt resistance gene in Escherichia coli., J Bacteriol. 187(8):2912-6

 [7] Higgins KA., Chivers PT., Maroney MJ., 2012, Role of the N-terminus in determining metal-specific responses in the E. coli Ni- and Co-responsive metalloregulator, RcnR., J Am Chem Soc. 134(16):7081-93

 [8] Higgins KA., Carr CE., Maroney MJ., 2012, Specific metal recognition in nickel trafficking., Biochemistry. 51(40):7816-32