RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: acrD
Gene(s): acrD   Genome Browser M3D Gene expression COLOMBOS
Note(s): During an experiment using increasing concentrations of tetracycline, the transcription of the acrD gene was induced in low concentrations (1.5 and 4 mg/L), but this induction decreased in high concentrations (10 mg/L) Viveiros M, Dupont M, Rodrigues L, Couto I, Davin-Regli A, Martins M, Pagès JM, Amaral L,2007 acrD expression is increased at least 5-fold by indole Hirakawa H,2005.
Promoter
Name: acrDp
+1: 2587475
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 120
Sequence: aaagtcagttaatgtaatgcctcctactgaccaaagaatacttgcacttaaggttcagtaTaaaagggcatgataatttac
                           -35                   -10        +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
Reference(s): [1] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[EvgA,+] 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 EvgA-phosphorylated activator acrDp 2587435 2587453 -31.5 aatgtaatgcCTCCTACTGACCAAAGAATacttgcactt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2]


Transcription unit          
Name: acrD
Gene(s): acrD   Genome Browser M3D Gene expression COLOMBOS
Note(s): During an experiment using increasing concentrations of tetracycline, the transcription of the acrD gene was induced in low concentrations (1.5 and 4 mg/L), but this induction decreased in high concentrations (10 mg/L) Viveiros M, Dupont M, Rodrigues L, Couto I, Davin-Regli A, Martins M, Pagès JM, Amaral L,2007 acrD expression is increased at least 5-fold by indole Hirakawa H,2005.
Promoter
Name: acrDp2
+1: 2587550
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 45
Sequence: atttacattaactcctttttttctccacgattggctcgtaccttgccgctacagtgaagcAagtcaagcctacaacgatac
                                -24         -12             +1                   
Note(s): This promoter was identified by microarray assays with a mutant σ54 strain and a σ54-overexpressing strain, and by σ54-related promoter element identification Zhao K,2010
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: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IEP]
Reference(s): [1] Huerta AM., et al., 2003
[3] Zhao K., et al., 2010
TF binding sites (TFBSs)
[BaeR,+] 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 BaeR-phosphorylated activator acrDp2 2587504 2587523 -36.5 acattaactcCTTTTTTTCTCCACGATTGGctcgtacctt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] W [4]
[CpxR,+] 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
remote CpxR-phosphorylated activator acrDp2 2587414 2587432 -127.5 ggagggtgagGAAAGTCAGTTAATGTAATgcctcctact nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] W [4]
remote CpxR-phosphorylated activator acrDp2 2587446 2587459 -98.0 tcctactgacCAAAGAATACTTGCacttaaggtt nd [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] W [4]
proximal CpxR-phosphorylated activator acrDp2 2587476 2587493 -66.0 ggttcagtatAAAAGGGCATGATAATTTacattaactc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] W [4]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [COMP-HINF] Inferred by a human based on computational evidence

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

 [EXP-IEP] Inferred from expression pattern

 [IC] Inferred by curator

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins


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] Hirakawa H., Nishino K., Yamada J., Hirata T., Yamaguchi A., 2003, Beta-lactam resistance modulated by the overexpression of response regulators of two-component signal transduction systems in Escherichia coli., J Antimicrob Chemother 52(4):576-82

 [3] Zhao K., Liu M., Burgess RR., 2010, Promoter and regulon analysis of nitrogen assimilation factor, sigma54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis., Nucleic Acids Res 38(4):1273-83

 [4] Hirakawa H., Inazumi Y., Masaki T., Hirata T., Yamaguchi A., 2005, Indole induces the expression of multidrug exporter genes in Escherichia coli., Mol Microbiol 55(4):1113-26

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