RegulonDB RegulonDB 11.0: Operon Form
   

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




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


Transcription unit          
Name: prpBCDE
Gene(s): prpB, prpC, prpD, prpE   Genome Browser M3D Gene expression COLOMBOS
Note(s): AscG may interfere with the activation of the prpBCDE operon by PrpR Ishida Y,2009
A new carbon catabolite repression (CCR) system was determined between carbohydrate-based carbon sources (sugars) and noncarbohydrate-based carbon sources (e.g., propionate).Expression of the prpBCDE operon is repressed in the presence of various sugars (arabinose, galactose, glucose, mannose, and xylose), and this repression is independent of sugar-specific regulators, such as AraC, cAMP-CRP, and the phosphotransferase system (PTS), during rapid sugar uptake and metabolism Park JM, Vinuselvi P, Lee SK,2012
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: prpBp
+1: 348646
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 36
Sequence: tgaaattaaacatttaattttattaaggcaattgtggcacaccccttgctttgtctttatCaacgcaaataacaagttgat
                                   -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: [AIBSCS]
[AIPP]
[ICWHO]
Reference(s): [1] Huerta AM., et al., 2003
[2] 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-cyclic-AMP activator prpBp 348529 348551 -106.5 acattgcctgAAACGTTAACTGAAACGCATATTtgcggattag nd [GEA], [APIORCISFBSCS], [BPP], [SM] [3]
[Cra,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Cra repressor prpBp 348536 348553 -101.5 ctgaaacgttAACTGAAACGCATATTTGcggattagtt nd [GEA], [AIBSCS] [4]
[PrpR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote PrpR-(2S,3S)-2-methylcitrate activator prpBp 348487 348510 -147.5 gtttagtcttGTTTCATAATTGTTGCAATGAAACgcggtgaaac nd [GEA], [APIORCISFBSCS] [3]
remote PrpR-(2S,3S)-2-methylcitrate activator prpBp 348521 348544 -113.5 gcggtgaaacATTGCCTGAAACGTTAACTGAAACgcatatttgc nd [APIORCISFBSCS] nd


Evidence    

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [AIPP] Automated inference of promoter position

 [ICWHO] Inferred computationally without human oversight

 [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

 [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] 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

 [3] 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

 [4] Shimada T., Yamamoto K., Ishihama A., 2011, Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli., J Bacteriol 193(3):649-59

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