RegulonDB RegulonDB 10.8: Operon Form
   

rcnAB operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: rcnAB
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: rcnAB
Gene(s): rcnA, rcnB   Genome Browser M3D Gene expression COLOMBOS
Note(s): In response to increasing concentrations of nickel or cobalt, RcnR releases the repression of rcnA and rcnR to allow its expression Iwig JS,2006. Iwig JS,2009 It has been recently determined that the expression levels of the rcnA and rcnR genes are directly induced by Ni and Co via the metallo-regulator RcnR, and both genes are differentially expressed Blaha D,2011
Evidence: [ICWHO] Inferred computationally without human oversight
[LTED] Length of transcript experimentally determined
Reference(s): [1] Bleriot C., et al., 2011
Promoter
Name: rcnAp
+1: 2185827
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 90
Sequence: tttctgtttatcacggattgtatgagacatggcaacacctggttaacaagaatatgaaaaAtcatagcactattaatctac
                      -35                       -10         +1                   
Evidence: [TIM]
Reference(s): [2] Blaha D., et al., 2011
TF binding sites (TFBSs)
[Fur,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Fur-Fe2+ repressor rcnAp 2185894 2185915 78.0 cagattgccgAATTAATACTAAGAATTATTATcatgaccgaa nd [AIBSCS], [APIORCISFBSCS], [CV(GEA/ROMA)], [GEA] [5]
remote Fur-Fe2+ repressor rcnAp 2185897 2185918 81.0 attgccgaatTAATACTAAGAATTATTATCATgaccgaattt nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [5]
remote Fur-Fe2+ repressor rcnAp 2185903 2185924 87.0 gaattaatacTAAGAATTATTATCATGACCGAatttacaact nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [5]
[RcnR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal RcnR1 repressor rcnAp 2185845 2185859 26.5 actattaatcTACTGGGGGGTAGTAtcaggtactg nd [BPP], [GEA] [2], [3], [4], [5]
remote RcnR2 repressor rcnAp 2185865 2185879 46.5 tagtatcaggTACTGGGGGGGAGTAgaatcagatt nd [BPP], [GEA] [2], [3], [4], [5]
Note(s): 1Bound RcnR (RcnR transcriptional repressor) represses transcription Iwig JS,2006. Koch D,2007. Iwig JS,2009 RcnR interacts nonspecifically with the approximately 50 bp flanking the core binding site, resulting in DNA wrapping and the introduction of a single negative supercoil into plasmid DNA Iwig JS,2009
2Bound RcnR (RcnR transcriptional repressor) represses transcription Iwig JS,2006. Koch D,2007. Iwig JS,2009 RcnR interacts nonspecifically with the approximately 50 bp flanking the core binding site, resulting in DNA wrapping and the introduction of a single negative supercoil into plasmid DNA Iwig JS,20091Bound RcnR (RcnR transcriptional repressor) represses transcription Iwig JS,2006. Koch D,2007. Iwig JS,2009 RcnR interacts nonspecifically with the approximately 50 bp flanking the core binding site, resulting in DNA wrapping and the introduction of a single negative supercoil into plasmid DNA Iwig JS,2009
2Bound RcnR (RcnR transcriptional repressor) represses transcription Iwig JS,2006. Koch D,2007. Iwig JS,2009 RcnR interacts nonspecifically with the approximately 50 bp flanking the core binding site, resulting in DNA wrapping and the introduction of a single negative supercoil into plasmid DNA Iwig JS,2009


Transcription unit       
Gene(s): rcnB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
[LTED] Length of transcript experimentally determined
Reference(s): [1] Bleriot C., et al., 2011


Regulation by sRNA    
  Small RNA name (Regulator) Regulation type Mechanism Function Binding Sites Evidence Reference
LeftPos RightPos Sequence (RNA-strand)
  omrB antisense post-transcriptional regulation repressor       [IMP] [6]
  omrA antisense post-transcriptional regulation repressor       [IMP] [6]
Notes: "The provided sequence is that of the RNA strand,i.e. 'U's are showed instead the 'T'"


Evidence    

 [TIM] Transcription initiation mapping

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [CV(GEA/ROMA)] cross validation(GEA/ROMA)

 [GEA] Gene expression analysis

 [BPP] Binding of purified proteins


Reference(s)    

 [1] Bleriot C., Effantin G., Lagarde F., Mandrand-Berthelot MA., Rodrigue A., 2011, RcnB is a periplasmic protein essential for maintaining intracellular Ni and Co concentrations in Escherichia coli., J Bacteriol 193(15):3785-93

 [2] 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

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

 [4] 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

 [5] 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

 [6] Guillier M., Gottesman S., 2008, The 5' end of two redundant sRNAs is involved in the regulation of multiple targets, including their own regulator., Nucleic Acids Res 36(21):6781-94

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