RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: rcnR
Gene(s): rcnR   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 In addition, in 2007 Koch et al. showed that the expression of this gene was affected positively by iron; it is uncertain whether this gene is activated by FUR Koch D,2007
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: rcnRp
+1: 2185903
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 107
Sequence: aagaaccaggcgtttccttgctgaagaagagttgtaaattcggtcatgataataattcttAgtattaattcggcaatctga
                             -35                       -10  +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Blaha D., et al., 2011
[2] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[RcnR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote RcnR repressor rcnRp 2185845 2185859 51.5 cagtacctgaTACTACCCCCCAGTAgattaatagt nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [3], [4], [5]
remote RcnR repressor rcnRp 2185865 2185879 31.5 aatctgattcTACTCCCCCCCAGTAcctgatacta nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [3], [4], [5]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis


Reference(s)    

 [1] 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

 [2] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [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

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