RegulonDB RegulonDB 11.2: 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 Vasilieva SV, Streltsova DA, Moshkovskaya EY, Sanina NA, Aldoshin SM,2010
Reference(s): [1] Landini P., et al., 1994
[2] Matijasevic Z., et al., 1992
[3] Volkert MR., et al., 1994
Promoter
Name: aidBp1
+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: [COMP-AINF]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
[EXP-IMP]
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)
[Ada,+] 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 Ada activator aidBp1 4414182 4414206 -53.5 cgcattacatTGCTGGATAAGAATGTTTTAGCAATctctttctgt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3], [8], [9]
[AidB,-] 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 AidB-isovaleryl-CoA repressor aidBp1 4414186 4414212 -48.0 ttacattgctGGATAAGAATGTTTTAGCAATCTCTTTctgtcatgaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [10]
[Lrp,-] 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
nd Lrp repressor aidBp1 nd nd nd nd nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [6]


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 Vasilieva SV, Streltsova DA, Moshkovskaya EY, Sanina NA, Aldoshin SM,2010
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: [COMP-AINF]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
[EXP-IMP]
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)
[Ada,+] 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 Ada activator aidBp2 4414182 4414206 -53.5 cgcattacatTGCTGGATAAGAATGTTTTAGCAATctctttctgt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3], [8], [9]
[AidB,-] 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 AidB-isovaleryl-CoA repressor aidBp2 4414186 4414212 -48.0 ttacattgctGGATAAGAATGTTTTAGCAATCTCTTTctgtcatgaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [10]
[Lrp,-] 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
nd Lrp repressor aidBp2 nd nd nd nd nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [6]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [EXP-IDA] Inferred from direct assay

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [EXP-IEP] Inferred from expression pattern

 [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


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