RegulonDB RegulonDB 10.10: Operon Form
   

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




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


Transcription unit          
Name: prpR
Gene(s): prpR   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: prpRp
+1: 348471
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 28
Sequence: tttcaggcaatgtttcaccgcgtttcattgcaacaattatgaaacaagactaaacccaatAttcggtttcttaactttgcg
                        -35                   -10           +1                   
Note(s): We assigned a putative transcription start site to this promoter based on the observation that the majority of the σ70-dependent promoters, whose transcription start sites were determined experimentally, present a distance of 7 nucleotides between the transcription start site and the -10 box Hawley DK, McClure WR,1983
Evidence: [HIPP]
[ICWHO]
Reference(s): [1] Huerta AM., et al., 2003
[2] Lee SK., et al., 2005
TF binding sites (TFBSs)
[AscG,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal AscG repressor prpRp 348487 348493 -18.5 tgcaacaattATGAAACaagactaaac nd [GEA], [AIBSCS], [BPP] [3]
proximal AscG repressor prpRp 348498 348504 -29.5 ccgcgtttcaTTGCAACaattatgaaa nd [GEA], [AIBSCS], [BPP] [3]
proximal AscG repressor prpRp 348505 348511 -36.5 tgtttcaccgCGTTTCAttgcaacaat nd [GEA], [AIBSCS], [BPP] [3]
proximal AscG repressor prpRp 348515 348521 -46.5 tttcaggcaaTGTTTCAccgcgtttca nd [GEA], [AIBSCS], [BPP] [3]
proximal AscG repressor prpRp 348527 348533 -58.5 tttcagttaaCGTTTCAggcaatgttt nd [GEA], [AIBSCS], [BPP] [3]
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cyclic-AMP activator prpRp 348529 348551 -68.5 ctaatccgcaAATATGCGTTTCAGTTAACGTTTcaggcaatgt nd [GEA], [APIORCISFBSCS], [BPP], [SM] [2], [3]
[PhoB,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal PhoB-phosphorylated repressor prpRp 348486 348504 -24.0 ccgcgtttcaTTGCAACAATTATGAAACAagactaaacc nd [GEA], [APIORCISFBSCS], [BPP] [4]
[PrpR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal PrpR-(2S,3S)-2-methylcitrate repressor prpRp 348487 348510 -27.5 gtttcaccgcGTTTCATTGCAACAATTATGAAACaagactaaac nd [GEA], [APIORCISFBSCS] [2]
proximal PrpR-(2S,3S)-2-methylcitrate repressor prpRp 348521 348544 -61.5 gcaaatatgcGTTTCAGTTAACGTTTCAGGCAATgtttcaccgc nd [APIORCISFBSCS] nd


Evidence    

 [HIPP] Human inference of promoter position

 [ICWHO] Inferred computationally without human oversight

 [GEA] Gene expression analysis

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins

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

 [SM] Site mutation


Reference(s)    

 [1] 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

 [2] Lee SK., Newman JD., Keasling JD., 2005, Catabolite repression of the propionate catabolic genes in Escherichia coli and Salmonella enterica: evidence for involvement of the cyclic AMP receptor protein., J Bacteriol 187(8):2793-800

 [3] Ishida Y., Kori A., Ishihama A., 2009, Participation of regulator AscG of the beta-glucoside utilization operon in regulation of the propionate catabolism operon., J Bacteriol 191(19):6136-44

 [4] Yang C., Huang TW., Wen SY., Chang CY., Tsai SF., Wu WF., Chang CH., 2012, Genome-wide PhoB binding and gene expression profiles reveal the hierarchical gene regulatory network of phosphate starvation in Escherichia coli., PLoS One 7(10):e47314

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