RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: araC
Synonym(s): OP00004
Gene(s): araC   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [1] Lee NL., et al., 1981
[2] Miyada CG., et al., 1984
Promoter
Name: araCp
+1: 70223
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 164
Sequence: tgacgccgtgcaaataatcaatgtggacttttctgccgtgattatagacacttttgttacGcgtttttgtcatggctttgg
                        -35                    -10          +1                   
Evidence: [COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Hamilton EP., et al., 1988
[4] Wallace RG., et al., 1980
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
remote AraC-α-L-arabinopyranose activator araCp 70110 70126 -105.0 ataaaaagcgTCAGGTAGGATCCGCTAatcttatgga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [5], [6], [7]
proximal AraC-α-L-arabinopyranose activator araCp 70131 70147 -84.0 ccgctaatctTATGGATAAAAATGCTAtggcatagca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [7]
[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 araCp 70131 70147 -84.0 ccgctaatctTATGGATAAAAATGCTAtggcatagca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [7]
proximal AraC-α-L-arabinopyranose repressor araCp 70184 70200 -31.0 aaataatcaaTGTGGACTTTTCTGCCGtgattataga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [9]
proximal AraC-α-L-arabinopyranose repressor araCp 70205 70221 -10.0 ctgccgtgatTATAGACACTTTTGTTAcgcgtttttg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [9], [11]
remote AraC repressor araCp 70342 70358 128.0 tctgatgcaaTATGGACAATTGGTTTCttctctgaat nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C nd
[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
proximal CRP-cyclic-AMP activator araCp 70158 70179 -54.5 tggcatagcaAAGTGTGACGCCGTGCAAATAAtcaatgtgga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [8]
[XylR,-] 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 XylR-α-D-xylopyranose repressor araCp 70195 70213 -19.5 gtggacttttCTGCCGTGATTATAGACACttttgttacg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [10]
proximal XylR-α-D-xylopyranose repressor araCp 70216 70234 2.5 atagacacttTTGTTACGCGTTTTTGTCAtggctttggt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [10]


Evidence    

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

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

 [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

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


Reference(s)    

 [1] 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

 [2] Miyada CG., Stoltzfus L., Wilcox G., 1984, Regulation of the araC gene of Escherichia coli: catabolite repression, autoregulation, and effect on araBAD expression., Proc Natl Acad Sci U S A 81(13):4120-4

 [3] 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

 [4] Wallace RG., Lee N., Fowler AV., 1980, The araC gene of Escherichia coli: transcriptional and translational start-points and complete nucleotide sequence., Gene 12(3-4):179-90

 [5] 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

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

 [7] 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

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

 [10] Koirala S., Wang X., Rao CV., 2015, Reciprocal Regulation of l-Arabinose and d-Xylose Metabolism in Escherichia coli., J Bacteriol 198(3):386-93

 [11] 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

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