RegulonDB RegulonDB 11.2: Operon Form
   

ada-alkB operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit       
Name: alkB
Synonym(s): OP00100
Gene(s): alkB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Kondo H., et al., 1986
Promoter
Name: alkBp
+1: 2309445
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 104
Sequence: aaagcggtacgggccgttgccagcgcctgtgccgccaacaagctggctatcataatacccTgtcatcgggtggtccgtggt
                                -35                  -10    +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
Reference(s): [2] Huerta AM., et al., 2003
[1] Kondo H., et al., 1986


Transcription unit          
Name: ada-alkB
Synonym(s): OP00100
Gene(s): alkB, ada   Genome Browser M3D Gene expression COLOMBOS
Note(s): Ada promotes transcription by EσS at both ada and aidB Landini P,1999
Evidence: [EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [1] Kondo H., et al., 1986
Promoter
Name: adap
+1: 2310427
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 22
Sequence: aaaaattaaagcgcaagattgttggtttttgcgtgatggtgaccgggcagcctaaaggctAtccttaaccagggagctgat
                                  -35                     -1+1                   
Evidence: [COMP-AINF]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
Reference(s): [2] Huerta AM., et al., 2003
[3] Landini P., et al., 1998
[4] Nakabeppu Y., et al., 1986
[5] Taverna P., et al., 1996
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 adap 2310474 2310498 -58.5 aaaagcttccTTGTCAGCGAAAAAAATTAAAGCGCaagattgttg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [7], [8], [9], [10], [11], [12], [13], [14]
[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 repressor adap 2310454 2310478 -38.5 aaaaaattaaAGCGCAAGATTGTTGGTTTTTGCGTgatggtgacc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [8], [9], [10], [12]


Transcription unit          
Name: ada-alkB
Synonym(s): OP00100
Gene(s): alkB, ada   Genome Browser M3D Gene expression COLOMBOS
Note(s): Ada promotes transcription by EσS at both ada and aidB Landini P,1999
Evidence: [EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [1] Kondo H., et al., 1986
Promoter
Name: adap2
+1: 2310427
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 22
Sequence: aaaaattaaagcgcaagattgttggtttttgcgtgatggtgaccgggcagcctaaaggctAtccttaaccagggagctgat
                                  -35                     -1+1                   
Evidence: [COMP-AINF]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
Reference(s): [2] Huerta AM., et al., 2003
[3] Landini P., et al., 1998
[4] Nakabeppu Y., et al., 1986
[5] Taverna P., et al., 1996
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 adap2 2310474 2310498 -58.5 aaaagcttccTTGTCAGCGAAAAAAATTAAAGCGCaagattgttg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [7], [8], [9], [10], [11], [12], [13], [14]
[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 repressor adap2 2310454 2310478 -38.5 aaaaaattaaAGCGCAAGATTGTTGGTTTTTGCGTgatggtgacc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [8], [9], [10], [12]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [EXP-IDA] Inferred from direct assay

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

 [EXP-IEP] Inferred from expression pattern

 [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] Kondo H., Nakabeppu Y., Kataoka H., Kuhara S., Kawabata S., Sekiguchi M., 1986, Structure and expression of the alkB gene of Escherichia coli related to the repair of alkylated DNA., J Biol Chem 261(33):15772-7

 [2] 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

 [3] 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

 [4] Nakabeppu Y., Sekiguchi M., 1986, Regulatory mechanisms for induction of synthesis of repair enzymes in response to alkylating agents: ada protein acts as a transcriptional regulator., Proc Natl Acad Sci U S A 83(17):6297-301

 [5] Taverna P., Sedgwick B., 1996, Generation of an endogenous DNA-methylating agent by nitrosation in Escherichia coli., J Bacteriol 178(17):5105-11

 [6] 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

 [7] 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

 [8] Nakamura T., Tokumoto Y., Sakumi K., Koike G., Nakabeppu Y., Sekiguchi M., 1988, Expression of the ada gene of Escherichia coli in response to alkylating agents. Identification of transcriptional regulatory elements., J Mol Biol 202(3):483-94

 [9] Saget BM., Shevell DE., Walker GC., 1995, Alteration of lysine 178 in the hinge region of the Escherichia coli ada protein interferes with activation of ada, but not alkA, transcription., J Bacteriol 177(5):1268-74

 [10] Saget BM., Walker GC., 1994, The Ada protein acts as both a positive and a negative modulator of Escherichia coli's response to methylating agents., Proc Natl Acad Sci U S A 91(21):9730-4

 [11] Sakumi K., Igarashi K., Sekiguchi M., Ishihama A., 1993, The Ada protein is a class I transcription factor of Escherichia coli., J Bacteriol 175(8):2455-7

 [12] Sakumi K., Sekiguchi M., 1989, Regulation of expression of the ada gene controlling the adaptive response. Interactions with the ada promoter of the Ada protein and RNA polymerase., J Mol Biol 205(2):373-85

 [13] Taketomi A., Nakabeppu Y., Ihara K., Hart DJ., Furuichi M., Sekiguchi M., 1996, Requirement for two conserved cysteine residues in the Ada protein of Escherichia coli for transactivation of the ada promoter., Mol Gen Genet 250(5):523-32

 [14] Teo I., Sedgwick B., Kilpatrick MW., McCarthy TV., Lindahl T., 1986, The intracellular signal for induction of resistance to alkylating agents in E. coli., Cell 45(2):315-24

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