RegulonDB RegulonDB 10.10: Operon Form
   

araE-ygeA operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: araE
Synonym(s): OP00103
Gene(s): araE   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Ebright RH., et al., 1985
[2] Heffernan L., et al., 1976
[3] Stringer AM., et al., 2014
Promoter
Name: araEp
+1: 2982208
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 26
Sequence: catatttatgctgtttccgacctgacacctgcgtgagttgttcacgtattttttcactatGtcttactctctgctggcagg
                      -35                      -10          +1                   
Evidence: [ICWHO]
[TIM]
Reference(s): [4] Huerta AM., et al., 2003
[5] Stoner C., et al., 1983
TF binding sites (TFBSs)
[AraC,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal AraC-α-L-arabinopyranose activator araEp 2982244 2982260 -44.0 tccatatttaTGCTGTTTCCGACCTGAcacctgcgtg nd [APIORCISFBSCS], [BPP] [5]
proximal AraC-α-L-arabinopyranose activator araEp 2982265 2982281 -65.0 cgacatgtcgCAGCAATTTAATCCATAtttatgctgt nd [APIORCISFBSCS], [BPP] [5]
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote CRP-cyclic-AMP activator araEp 2982292 2982313 -94.5 ttaatttgaaAATTGGAATATCCATCACATAAcgacatgtcg nd [AIBSCS], [BPP] [5]


Transcription unit          
Name: araE-ygeA
Gene(s): ygeA, araE   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [3] Stringer AM., et al., 2014
Promoter
Name: araEp
+1: 2982208
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 26
Sequence: catatttatgctgtttccgacctgacacctgcgtgagttgttcacgtattttttcactatGtcttactctctgctggcagg
                      -35                      -10          +1                   
Evidence: [ICWHO]
[TIM]
Reference(s): [4] Huerta AM., et al., 2003
[5] Stoner C., et al., 1983
TF binding sites (TFBSs)
[AraC,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal AraC-α-L-arabinopyranose activator araEp 2982244 2982260 -44.0 tccatatttaTGCTGTTTCCGACCTGAcacctgcgtg nd [APIORCISFBSCS], [BPP] [5]
proximal AraC-α-L-arabinopyranose activator araEp 2982265 2982281 -65.0 cgacatgtcgCAGCAATTTAATCCATAtttatgctgt nd [APIORCISFBSCS], [BPP] [5]
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote CRP-cyclic-AMP activator araEp 2982292 2982313 -94.5 ttaatttgaaAATTGGAATATCCATCACATAAcgacatgtcg nd [AIBSCS], [BPP] [5]


Transcription unit       
Name: ygeA
Gene(s): ygeA   Genome Browser M3D Gene expression COLOMBOS
Note(s): A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for ygeA. This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [ICWHO] Inferred computationally without human oversight
[LTED] Length of transcript experimentally determined
Reference(s): [3] Stringer AM., et al., 2014


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -21.6 2980724 2980757 ctgatttcacGGGCCGGATGTGCTGTACATCCGGCCCTTTTTTcgttaataga
  terminator -6.5 2982214 2982239 acctgacaccTGCGTGAGTTGTTCACGTATTTTTTcactatgtct
  anti-terminator -7.4 2980747 2980777 aagttgagaaATATCGGCGTCTGATTTCACGGGCCGGATGtgctgtacat
  anti-terminator -7.1 2982231 2982265 tttaatccatATTTATGCTGTTTCCGACCTGACACCTGCGTGAGttgttcacgt
  anti-anti-terminator -9.0 2980765 2980795 aaactgatggCAGGCGAGAAGTTGAGAAATATCGGCGTCTgatttcacgg
  anti-anti-terminator -4.99 2982255 2982282 acgacatgtcGCAGCAATTTAATCCATATTTATGCTGtttccgacct
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    

 [ICWHO] Inferred computationally without human oversight

 [TIM] Transcription initiation mapping

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [BPP] Binding of purified proteins

 [AIBSCS] Automated inference based on similarity to consensus sequences


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] Heffernan L., Bass R., Englesberg E., 1976, Mutations affecting catabolite repression of the L-arabinose regulon in Escherichia coli B/r., J Bacteriol 126(3):1119-31

 [3] Stringer AM., Currenti S., Bonocora RP., Baranowski C., Petrone BL., Palumbo MJ., Reilly AA., Zhang Z., Erill I., Wade JT., 2014, Genome-scale analyses of Escherichia coli and Salmonella enterica AraC reveal noncanonical targets and an expanded core regulon., J Bacteriol 196(3):660-71

 [4] 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

 [5] Stoner C., Schleif R., 1983, The araE low affinity L-arabinose transport promoter. Cloning, sequence, transcription start site and DNA binding sites of regulatory proteins., J Mol Biol 171(4):369-81

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