RegulonDB RegulonDB 11.2: 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): The pck expression is induced when the cell is grown on acetate, pyruvate, or glycerol El-Mansi M, Phue JN, Shiloach J,2021.
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                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA]
[EXP-IMP]
Reference(s): [3] Huerta AM., et al., 2003
[4] Prost JF., et al., 1999
TF binding sites (TFBSs)
[CRP,+] 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
proximal CRP-cyclic-AMP activator pckp 3532581 3532597 -90.5 cattcaggaaTGCGATTCCACTCACAAtattcccgcc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [6], [7]
[CRP,-] 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
proximal CRP-cyclic-AMP repressor pckp 3532684 3532700 13.5 gcaaccgtttCGTGACAGGAATCACGGagttttttgt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [6]
[Cra,+] 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 Cra activator pckp 3532531 3532548 -139.5 aaagttagcgTGGTGAATCGATACTTTAccggttgaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [5]
[DcuR,+] 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
proximal DcuR-phosphorylated activator pckp 3532607 3532624 -64.0 atattcccgcCATATAAACCAAGATTTAaccttttgag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [7]
proximal DcuR-phosphorylated activator pckp 3532658 3532675 -13.0 cctaaaatgcTATTTCTGCGATAATAGCaaccgtttcg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [7]


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"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [EXP-IDA] Inferred from direct assay

 [EXP-IMP] Inferred from mutant phenotype

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

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

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

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Oh MK., Liao JC., 2000, Gene expression profiling by DNA microarrays and metabolic fluxes in Escherichia coli., Biotechnol Prog 16(2):278-86

 [2] Sabnis NA., Yang H., Romeo T., 1995, Pleiotropic regulation of central carbohydrate metabolism in Escherichia coli via the gene csrA., J Biol Chem 270(49):29096-104

 [3] 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

 [4] Prost JF., Cozzone AJ., 1999, Detection of an extended-10 element in the promoter region of the pckA gene encoding phosphoenolpyruvate carboxykinase in Escherichia coli., Biochimie 81(3):197-200

 [5] Ramseier TM., Bledig S., Michotey V., Feghali R., Saier MH., 1995, The global regulatory protein FruR modulates the direction of carbon flow in Escherichia coli., Mol Microbiol 16(6):1157-69

 [6] Nakano M., Ogasawara H., Shimada T., Yamamoto K., Ishihama A., 2014, Involvement of cAMP-CRP in transcription activation and repression of the pck gene encoding PEP carboxykinase, the key enzyme of gluconeogenesis., FEMS Microbiol Lett 355(2):93-9

 [7] Surmann K., Stopp M., Worner S., Dhople VM., Volker U., Unden G., Hammer E., 2020, Fumarate dependent protein composition under aerobic and anaerobic growth conditions in Escherichia coli., J Proteomics 212:103583

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