RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: pck
Synonym(s): OP00192
Gene(s): pck   Genome Browser M3D Gene expression COLOMBOS
Note(s): CRP binds to two sites in the pckp promoter that control its expression. These are called box 1 (-90.5) and box 2 (+13.5). cAMP-CRP binds to CRP box 1 at low cAMP-CRP concentrations and to both box 1 and box 2 at high concentrations Nakano M,2014
Reference(s): [1] Oh MK., et al., 2000
[2] Sabnis NA., et al., 1995
Promoter
Name: pckp
+1: 3532679
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 139
Sequence: gatttaaccttttgagaacattttccacacctaaaatgctatttctgcgataatagcaacCgtttcgtgacaggaatcacg
                      -35                        -10        +1                   
Note(s): The promoter for pck contains an extended -10 element.
Evidence: [HIPP]
[ICWHO]
[IDA]
[IMP]
Reference(s): [3] Huerta AM., et al., 2003
[4] Prost JF., et al., 1999
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP1 activator pckp 3532581 3532597 -90.5 cattcaggaaTGCGATTCCACTCACAAtattcccgcc nd [APIORCISFBSCS], [BPP], [GEA] [6], [7]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP1 repressor pckp 3532684 3532700 13.5 gcaaccgtttCGTGACAGGAATCACGGagttttttgt nd [APIORCISFBSCS], [BPP], [GEA] [6]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Cra1 activator pckp 3532531 3532548 -139.5 aaagttagcgTGGTGAATCGATACTTTACcggttgaatt nd [APIORCISFBSCS], [BPP], [GEA], [SM] [5]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal DcuR-phosphorylated1 activator pckp 3532607 3532624 -64.0 atattcccgcCATATAAACCAAGATTTAaccttttgag nd [APIORCISFBSCS], [GEA] [7]
proximal DcuR-phosphorylated2 activator pckp 3532658 3532675 -13.0 cctaaaatgcTATTTCTGCGATAATAGCaaccgtttcg nd [APIORCISFBSCS], [GEA] [7]
Note(s): 1CRP box 1 (-90.5) activates pck expression only in the presence of low levels of cAMP-CRP Nakano M,2014 However, the activation of pck by CRP is not clear, based on in vitro experiments. It is possible that there is a yet-unidentified supporting factor for transcription activation in vivo of the pck gene, as in the case of Cra, which positively regulates the expression of pck Ramseier TM,19951CRP box 2 (+13.5) represses pck expression only in the presence of high levels of cAMP-CRP Nakano M,20141As an earlier study had described a negative effect in a fruR mutant of S. enterica serovar Typhimurium for the expression of pckA 2496106, it was inferred that FruR could activate pckA transcription. Now as the FruR site was found 145 bp upstream of the transcriptional start site (similar to the ace operon site), the suggestion is that FruR is able to activate gene expression at a considerable distance, possibly looping the DNA in order to contact the transcriptional initiation complex.1DcuR appears to affect the expression of pck in response to fumarate Surmann K,2020.
2DcuR appears to affect the expression of pck in response to fumarate Surmann K,2020.1As an earlier study had described a negative effect in a fruR mutant of S. enterica serovar Typhimurium for the expression of pckA 2496106, it was inferred that FruR could activate pckA transcription. Now as the FruR site was found 145 bp upstream of the transcriptional start site (similar to the ace operon site), the suggestion is that FruR is able to activate gene expression at a considerable distance, possibly looping the DNA in order to contact the transcriptional initiation complex.
2CRP box 1 (-90.5) activates pck expression only in the presence of low levels of cAMP-CRP Nakano M,2014 However, the activation of pck by CRP is not clear, based on in vitro experiments. It is possible that there is a yet-unidentified supporting factor for transcription activation in vivo of the pck gene, as in the case of Cra, which positively regulates the expression of pck Ramseier TM,1995
3DcuR appears to affect the expression of pck in response to fumarate Surmann K,2020.
4DcuR appears to affect the expression of pck in response to fumarate Surmann K,2020.
5CRP box 2 (+13.5) represses pck expression only in the presence of high levels of cAMP-CRP Nakano M,2014


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -6.7 3532681 3532710 tagcaaccgtTTCGTGACAGGAATCACGGAGTTTTTTGTcaaatatgaa
  anti-terminator -7.2 3532643 3532692 gaacattttcCACACCTAAAATGCTATTTCTGCGATAATAGCAACCGTTTCGTGACAGGaatcacggag
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"





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