RegulonDB RegulonDB 10.8: 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: [TIM]
Reference(s): [3] Lee N., et al., 1977
[4] Lisser S., et al., 1993
[5] Smith BR., et al., 1978
Terminator(s)
Type: rho-independent
Sequence: ccatcaaaaaACCAGGCTTGAGTATAGCCTGGtttcgtttga
Reference(s): [6] Lee N., et al., 1986
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 AraC-arabinose activator araBp 70110 70126 -43.0 tccataagatTAGCGGATCCTACCTGAcgctttttat nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [7], [8], [11], [12], [13], [16], [19], [20]
proximal AraC-arabinose activator araBp 70131 70147 -64.0 tgctatgccaTAGCATTTTTATCCATAagattagcgg nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [7], [9], [10], [11], [12], [13], [19], [20]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal AraC repressor araBp 70131 70147 -64.0 tgctatgccaTAGCATTTTTATCCATAagattagcgg nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [7], [9], [10], [11], [12], [13], [19], [20]
remote AraC-arabinose repressor araBp 70184 70200 -117.0 tctataatcaCGGCAGAAAAGTCCACAttgattattt nd [APIORCISFBSCS], [BCE], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [7], [10], [14]
remote AraC-arabinose repressor araBp 70205 70221 -138.0 caaaaacgcgTAACAAAAGTGTCTATAatcacggcag nd [APIORCISFBSCS], [BCE], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [7], [10], [14]
remote AraC repressor araBp 70342 70358 -275.0 attcagagaaGAAACCAATTGTCCATAttgcatcaga nd [APIORCISFBSCS], [BCE], [BPP], [CV(SM)], [SM] [7], [8], [9], [10], [11], [12], [13]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote CRP-cAMP activator araBp 70158 70179 -93.5 tccacattgaTTATTTGCACGGCGTCACACTTtgctatgcca nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [8], [11], [15], [16], [17], [18]


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"




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] 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

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

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

 [6] 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

 [7] Gallegos MT., Schleif R., Bairoch A., Hofmann K., Ramos JL., 1997, Arac/XylS family of transcriptional regulators., Microbiol Mol Biol Rev 61(4):393-410

 [8] Huo L., Martin KJ., Schleif R., 1988, Alternative DNA loops regulate the arabinose operon in Escherichia coli., Proc Natl Acad Sci U S A 85(15):5444-8

 [9] Lee DH., Schleif RF., 1989, In vivo DNA loops in araCBAD: size limits and helical repeat., Proc Natl Acad Sci U S A 86(2):476-80

 [10] Lee NL., Gielow WO., Wallace RG., 1981, Mechanism of araC autoregulation and the domains of two overlapping promoters, Pc and PBAD, in the L-arabinose regulatory region of Escherichia coli., Proc Natl Acad Sci U S A 78(2):752-6

 [11] 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

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

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

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

 [15] Hamilton EP., Lee N., 1988, Three binding sites for AraC protein are required for autoregulation of araC in Escherichia coli., Proc Natl Acad Sci U S A 85(6):1749-53

 [16] Lee N., Francklyn C., Hamilton EP., 1987, Arabinose-induced binding of AraC protein to araI2 activates the araBAD operon promoter., Proc Natl Acad Sci U S A 84(24):8814-8

 [17] 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

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

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

 [20] 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


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