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RcnR DNA-binding transcriptional repressor

Synonyms: RcnR-Ni2+, RcnR, RcnR-Co2+
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) [1], that regulate the transcriptional expression of a recently described efflux protein, RcnA [6], to maintain nickel and cobalt homeostasis [1, 2]. 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 [1]. Ni(II) and Co(II) binding results in the transcription of RcnAB in vivo, although it has been shown that RcnR binds a variety of metal ions in vitro [4].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
Evolutionary Family: RcnR_FrmR_like_DUF156
TFBs length: 15
TFBs symmetry: inverted-repeat
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)
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 Confidence level (C: Confirmed, S: Strong, W: Weak) References
  RcnR repressor rcnAp Sigma70 26.5 -64.5 rcnA, rcnB
2185845 2185859 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1], [2], [3], [3], [4], [4], [5]
  RcnR repressor rcnAp Sigma70 46.5 -44.5 rcnA, rcnB
2185865 2185879 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1], [2], [3], [3], [4], [4], [5]
  RcnR repressor rcnRp Sigma70 31.5 -76.5 rcnR
  RcnR repressor rcnRp Sigma70 51.5 -56.5 rcnR

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


 [1] 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

 [2] 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

 [3] Blaha D., Arous S., Bleriot C., Dorel C., Mandrand-Berthelot MA., Rodrigue A., 2011, 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 93(3):434-9

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

 [5] Baumgart LA, Lee JE, Salamov A, Dilworth DJ, Na H, Mingay M, Blow MJ, Zhang Y, Yoshinaga Y, Daum CG, O'Malley RC, 2021, Persistence and plasticity in bacterial gene regulation., Nat Methods, 18(12):1499 10.1038/s41592-021-01312-2

 [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 10.1128/JB.187.8.2912-2916.2005

 [7] Huang HT, Bobst CE, Iwig JS, Chivers PT, Kaltashov IA, Maroney MJ, 2018, Co(II) and Ni(II) binding of the Escherichia coli transcriptional repressor RcnR orders its N terminus, alters helix dynamics, and reduces DNA affinity., J Biol Chem, 293(1):324 10.1074/jbc.RA117.000398

 [8] 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 10.1021/ja300834b

 [9] 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 10.1021/ja710067d

 [10] Carr CE, Musiani F, Huang HT, Chivers PT, Ciurli S, Maroney MJ, 2017, Glutamate Ligation in the Ni(II)- and Co(II)-Responsive Escherichia coli Transcriptional Regulator, RcnR., Inorg Chem, 56(11):6459 10.1021/acs.inorgchem.7b00527

 [11] Li C, Vavra JW, Carr CE, Huang HT, Maroney MJ, Wilmot CM, 2020, Complexation of the nickel and cobalt transcriptional regulator RcnR with DNA., Acta Crystallogr F Struct Biol Commun, 76(Pt 1):25 10.1107/S2053230X19017084

 [12] Huang HT, Maroney MJ, 2019, Ni(II) Sensing by RcnR Does Not Require an FrmR-Like Intersubunit Linkage., Inorg Chem, 58(20):13639 10.1021/acs.inorgchem.9b01096

 [13] Higgins KA, Carr CE, Maroney MJ, 2012, Specific metal recognition in nickel trafficking., Biochemistry, 51(40):7816 10.1021/bi300981m