RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: araBAD
Synonym(s): OP00302, ara
Gene(s): araD, araA, araB   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [1] Ebright RH., et al., 1985
[2] Reeder T., et al., 1991
Promoter
Name: araBp
+1: 70075
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 27
Sequence: ccataagattagcggatcctacctgacgctttttatcgcaactctctactgtttctccatAcccgtttttttggatggagt
                            -35                     -10     +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Huerta AM., et al., 2003
[4] Lee N., et al., 1977
[5] Lisser S., et al., 1993
[6] Smith BR., et al., 1978
Terminator(s)
Type: rho-independent
Sequence: ccatcaaaaaACCAGGCTTGAGTATAGCCTGGtttcgtttga
Reference(s): [7] Lee N., et al., 1986
TF binding sites (TFBSs)
[AraC,+] 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 AraC-α-L-arabinopyranose activator araBp 70110 70126 -43.0 tccataagatTAGCGGATCCTACCTGAcgctttttat 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], [14], [15]
proximal AraC-α-L-arabinopyranose activator araBp 70131 70147 -64.0 tgctatgccaTAGCATTTTTATCCATAagattagcgg 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], [14], [15]
[AraC,-] 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 AraC repressor araBp 70131 70147 -64.0 tgctatgccaTAGCATTTTTATCCATAagattagcgg 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], [14], [15]
remote AraC-α-L-arabinopyranose repressor araBp 70184 70200 -117.0 tctataatcaCGGCAGAAAAGTCCACAttgattattt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [11]
remote AraC-α-L-arabinopyranose repressor araBp 70205 70221 -138.0 caaaaacgcgTAACAAAAGTGTCTATAatcacggcag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [11]
remote AraC repressor araBp 70342 70358 -275.0 attcagagaaGAAACCAATTGTCCATAttgcatcaga nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [8], [9], [10]
[CRP,+] 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 CRP-cyclic-AMP activator araBp 70158 70179 -93.5 tccacattgaTTATTTGCACGGCGTCACACTTtgctatgcca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [8], [12], [13]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -12.7 66677 66716 cctgatgcgaCGCTGGCGCGTCTTATCAGGCCTACGCGCTGCGATTTTGtaggccggat
  terminator -10.0 70049 70086 aactctctacTGTTTCTCCATACCCGTTTTTTTGGATGGAGTGAAACgatggcgatt
  anti-terminator -6.2 66705 66718 cgcctgatgcGACGCTGGCGCGTcttatcaggc
  anti-anti-terminator -19.92 66710 66759 gattttgtagGCCGGATAAGCAAAGCGCATCCGGCATTCAACGCCTGATGCGACGCTGGcgcgtcttat
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [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

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts


Reference(s)    

 [1] Ebright RH., Beckwith J., 1985, The catabolite gene activator protein (CAP) is not required for indole-3-acetic acid to activate transcription of the araBAD operon of Escherichia coli K-12., Mol Gen Genet 201(1):51-5

 [2] Reeder T., Schleif R., 1991, Mapping, sequence, and apparent lack of function of araJ, a gene of the Escherichia coli arabinose regulon., J Bacteriol 173(24):7765-71

 [3] 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

 [4] Lee N., Carbon J., 1977, Nucleotide sequence of the 5' end of araBAD operon messenger RNA in Escherichia coli B/r., Proc Natl Acad Sci U S A 74(1):49-53

 [5] Lisser S., Margalit H., 1993, Compilation of E. coli mRNA promoter sequences., Nucleic Acids Res 21(7):1507-16

 [6] Smith BR., Schleif R., 1978, Nucleotide sequence of the L-arabinose regulatory region of Escherichia coli K12., J Biol Chem 253(19):6931-3

 [7] Lee N., Gielow W., Martin R., Hamilton E., Fowler A., 1986, The organization of the araBAD operon of Escherichia coli., Gene 47(2-3):231-44

 [8] Lobell RB., Schleif RF., 1991, AraC-DNA looping: orientation and distance-dependent loop breaking by the cyclic AMP receptor protein., J Mol Biol 218(1):45-54

 [9] Niland P., Huhne R., Muller-Hill B., 1996, How AraC interacts specifically with its target DNAs., J Mol Biol 264(4):667-74

 [10] Seabold RR., Schleif RF., 1998, Apo-AraC actively seeks to loop., J Mol Biol 278(3):529-38

 [11] Lee DH., Huo L., Schleif R., 1992, Repression of the araBAD promoter from araO1., J Mol Biol 224(2):335-41

 [12] Stoltzfus L., Wilcox G., 1989, Effect of mutations in the cyclic AMP receptor protein-binding site on araBAD and araC expression., J Bacteriol 171(2):1178-84

 [13] Zhang X., Schleif R., 1998, Catabolite gene activator protein mutations affecting activity of the araBAD promoter., J Bacteriol 180(2):195-200

 [14] Bustos SA., Schleif RF., 1993, Functional domains of the AraC protein., Proc Natl Acad Sci U S A 90(12):5638-42

 [15] Reeder T., Schleif R., 1993, AraC protein can activate transcription from only one position and when pointed in only one direction., J Mol Biol 231(2):205-18

RegulonDB