RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: aidB
Synonym(s): OP00135
Gene(s): aidB   Genome Browser M3D Gene expression COLOMBOS
Note(s): Ada promotes transcription by EσS at both ada and aidB Landini P,1999
A new signaling function of nitric oxide regulating the expression of the aidB gene under anaerobic conditions by FNR has been reported 20714851
Reference(s): [1] Landini P., et al., 1994
[2] Matijasevic Z., et al., 1992
[3] Volkert MR., et al., 1994
Promoter
Name: aidBp
+1: 4414247
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 28
Sequence: gataagaatgttttagcaatctctttctgtcatgaatccatggcagtgaccatactaatgGtgactgccattgatggaggg
                        -35                        -10      +1                   
Note(s): In the aidB promoter, EσS, but not Eσ70, can recognize with equal efficiency either C or T as the first nucleotide in the -10 promoter element Lacour S,2003
Evidence: [ICWHO]
[TIM]
Reference(s): [4] Huerta AM., et al., 2003
[5] Landini P., et al., 1998
[6] Landini P., et al., 1996
[1] Landini P., et al., 1994
[7] Maciag A., et al., 2011
[3] Volkert MR., et al., 1994
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 Ada1 activator aidBp 4414182 4414206 -53.5 cgcattacatTGCTGGATAAGAATGTTTTAGCAATctctttctgt nd [APIORCISFBSCS], [BPP], [GEA] [3], [8], [9]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal AidB-isovaleryl-CoA repressor aidBp 4414186 4414212 -48.0 ttacattgctGGATAAGAATGTTTTAGCAATCTCTTTctgtcatgaa nd [BPP], [GEA] [10]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Lrp1 repressor aidBp nd nd nd nd nd [BPP], [GEA], [IGI] [6]
Note(s): 1Evidence supports the existence of a regulatory element controlling induction under oxygen-limiting conditions in aidB. The aidB mRNA start site is identical whether induction occurs via Ada-dependent or Ada-independent pathway.1Lrp is a specific repressor for σ38-dependent transcription of the aidB promoter. Activation of the aidB promoter by Ada is dominant over repression by Lrp in vitro.1Evidence supports the existence of a regulatory element controlling induction under oxygen-limiting conditions in aidB. The aidB mRNA start site is identical whether induction occurs via Ada-dependent or Ada-independent pathway.
3Lrp is a specific repressor for σ38-dependent transcription of the aidB promoter. Activation of the aidB promoter by Ada is dominant over repression by Lrp in vitro.


Transcription unit          
Name: aidB
Synonym(s): OP00135
Gene(s): aidB   Genome Browser M3D Gene expression COLOMBOS
Note(s): Ada promotes transcription by EσS at both ada and aidB Landini P,1999
A new signaling function of nitric oxide regulating the expression of the aidB gene under anaerobic conditions by FNR has been reported 20714851
Reference(s): [1] Landini P., et al., 1994
[2] Matijasevic Z., et al., 1992
[3] Volkert MR., et al., 1994
Promoter
Name: aidBp2
+1: 4414247
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 28
Sequence: gataagaatgttttagcaatctctttctgtcatgaatccatggcagtgaccatactaatgGtgactgccattgatggaggg
                             -35              -10           +1                   
Note(s): In the aidB promoter, EσS, but not Eσ70, can recognize with equal efficiency either C or T as the first nucleotide in the -10 promoter element Lacour S,2003
Evidence: [ICWHO]
[TIM]
Reference(s): [4] Huerta AM., et al., 2003
[5] Landini P., et al., 1998
[6] Landini P., et al., 1996
[1] Landini P., et al., 1994
[7] Maciag A., et al., 2011
[3] Volkert MR., et al., 1994
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 Ada1 activator aidBp2 4414182 4414206 -53.5 cgcattacatTGCTGGATAAGAATGTTTTAGCAATctctttctgt nd [APIORCISFBSCS], [BPP], [GEA] [3], [8], [9]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal AidB-isovaleryl-CoA repressor aidBp2 4414186 4414212 -48.0 ttacattgctGGATAAGAATGTTTTAGCAATCTCTTTctgtcatgaa nd [BPP], [GEA] [10]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Lrp1 repressor aidBp2 nd nd nd nd nd [BPP], [GEA], [IGI] [6]
Note(s): 1Evidence supports the existence of a regulatory element controlling induction under oxygen-limiting conditions in aidB. The aidB mRNA start site is identical whether induction occurs via Ada-dependent or Ada-independent pathway.1Lrp is a specific repressor for σ38-dependent transcription of the aidB promoter. Activation of the aidB promoter by Ada is dominant over repression by Lrp in vitro.1Evidence supports the existence of a regulatory element controlling induction under oxygen-limiting conditions in aidB. The aidB mRNA start site is identical whether induction occurs via Ada-dependent or Ada-independent pathway.
3Lrp is a specific repressor for σ38-dependent transcription of the aidB promoter. Activation of the aidB promoter by Ada is dominant over repression by Lrp in vitro.




Reference(s)    

 [1] Landini P., Hajec LI., Volkert MR., 1994, Structure and transcriptional regulation of the Escherichia coli adaptive response gene aidB., J Bacteriol 176(21):6583-9

 [2] Matijasevic Z., Hajec LI., Volkert MR., 1992, Anaerobic induction of the alkylation-inducible Escherichia coli aidB gene involves genes of the cysteine biosynthetic pathway., J Bacteriol 174(6):2043-6

 [3] Volkert MR., Hajec LI., Matijasevic Z., Fang FC., Prince R., 1994, Induction of the Escherichia coli aidB gene under oxygen-limiting conditions requires a functional rpoS (katF) gene., J Bacteriol 176(24):7638-45

 [4] 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

 [5] Landini P., Bown JA., Volkert MR., Busby SJ., 1998, Ada protein-RNA polymerase sigma subunit interaction and alpha subunit-promoter DNA interaction are necessary at different steps in transcription initiation at the Escherichia coli Ada and aidB promoters., J Biol Chem 273(21):13307-12

 [6] Landini P., Hajec LI., Nguyen LH., Burgess RR., Volkert MR., 1996, The leucine-responsive regulatory protein (Lrp) acts as a specific repressor for sigma s-dependent transcription of the Escherichia coli aidB gene., Mol Microbiol 20(5):947-55

 [7] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55

 [8] Landini P., Volkert MR., 1995, RNA polymerase alpha subunit binding site in positively controlled promoters: a new model for RNA polymerase-promoter interaction and transcriptional activation in the Escherichia coli ada and aidB genes., EMBO J 14(17):4329-35

 [9] Landini P., Volkert MR., 1995, Transcriptional activation of the Escherichia coli adaptive response gene aidB is mediated by binding of methylated Ada protein. Evidence for a new consensus sequence for Ada-binding sites., J Biol Chem 270(14):8285-9

 [10] Rippa V., Amoresano A., Esposito C., Landini P., Volkert M., Duilio A., 2010, Specific DNA binding and regulation of its own expression by the AidB protein in Escherichia coli., J Bacteriol 192(23):6136-42


RegulonDB