RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: zraSR
Synonym(s): hydHG
Gene(s): zraS, zraR   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IEP] Inferred from expression pattern
[ITCR] Inferred through co-regulation
Reference(s): [1] Stoker K., et al., 1989
Promoter
Name: zraSp
+1: 4201905
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 21
Sequence: tgtgttacagcgcagggtaagcgctgataaaagatggcatgatttctgctgtcagaaaggGatgagcaggcaaagaagaag
                                   -24         -12          +1                   
Note(s): We assigned a putative transcription start site to this promoter based on the observation that the majority of the σ54-dependent promoters, whose transcription start sites were determined experimentally, present a distance of 11 nucleotides between the transcription start site and the -12 box Barrios H,1999.
Evidence: [AIPP]
[HIPP]
[ICWHO]
Reference(s): [2] Huerta AM., et al., 2003
[3] Leonhartsberger S., et al., 2001
[4] Reitzer L., et al., 2001
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote CRP-cAMP activator zraSp 4201671 4201692 -223.5 ccagggcaatTTTCGTGTTCCGTTTCATGGTTAatcctccagt nd [AIBSCS], [GEA] [5]
[ZraR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote ZraR-phosphorylated activator zraSp 4201782 4201798 -115.0 catgataaacGAGTAAAAATGACTCGCCtgctgcgggt nd [APIORCISFBSCS], [BPP], [GEA], [APIORCISFBSCS], [BPP], [GEA] [3]
proximal ZraR-phosphorylated2 activator zraSp 4201811 4201827 -86.0 gctgcgggtaGCGAGTCATTTTTACTCAttgaaactta nd [BPP], [GEA] [3]
Note(s): 2ZraR activates the zraSp promoter in the presence of high Zn2+ and Pb2+ concentrationsLeonhartsberger S,2001.3ZraR activates the zraSp promoter in the presence of high Zn2+ and Pb2+ concentrationsLeonhartsberger S,2001.


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -14.5 4201791 4201824 gagtaaaaatGACTCGCCTGCTGCGGGTAGCGAGTCATTTTTActcattgaaa
  anti-terminator -5.3 4201770 4201803 gggtaatctgGCATGATAAACGAGTAAAAATGACTCGCCTGCTgcgggtagcg
  anti-anti-terminator -11.8 4201733 4201775 tgcatcttccGTGCCAACGATGAAACGCTGATATGACGGGTAATCTGGCATGataaacgagt
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

 [AIPP] Automated inference of promoter position

 [HIPP] Human inference of promoter position

 [ICWHO] Inferred computationally without human oversight

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [GEA] Gene expression analysis

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

 [BPP] Binding of purified proteins


Reference(s)    

 [1] Stoker K., Reijnders WN., Oltmann LF., Stouthamer AH., 1989, Initial cloning and sequencing of hydHG, an operon homologous to ntrBC and regulating the labile hydrogenase activity in Escherichia coli K-12., J Bacteriol 171(8):4448-56

 [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] Leonhartsberger S., Huber A., Lottspeich F., Bock A., 2001, The hydH/G Genes from Escherichia coli code for a zinc and lead responsive two-component regulatory system., J Mol Biol 307(1):93-105

 [4] Reitzer L., Schneider BL., 2001, Metabolic context and possible physiological themes of sigma(54)-dependent genes in Escherichia coli., Microbiol Mol Biol Rev 65(3):422-44, table of contents

 [5] Zheng D., Constantinidou C., Hobman JL., Minchin SD., 2004, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling., Nucleic Acids Res 32(19):5874-93

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