RegulonDB RegulonDB 10.10: Operon Form
   

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




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


Transcription unit          
Name: hcaR
Gene(s): hcaR   Genome Browser M3D Gene expression COLOMBOS
Note(s): The hcaR gene appears to be negatively regulated by ArcA in an indirect way. The regulatory region of the hcaR gene has a putative ArcA-binding site, but when it is partially deleted, the effect of ArcA on the gene is not lost Turlin E,2005.
Promoter
Name: hcaRp
+1: 2668964
Distance from start of the gene: 68
Sequence: aatcctgaaagataagatgtattgaccttctatttttgtgccataaggatgttgctggttGgttgctaatatgtgaaatag
Note(s): The hcaRp promoter has a weak -10 region (AAGGAT) and a good -35 region (TTGACC) Turlin E,2005.
Evidence: [TIM]
Reference(s): [1] Turlin E., et al., 2005
TF binding sites (TFBSs)
[HcaR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal HcaR repressor hcaRp 2668934 2668946 25.0 atatgtgaaaTAGTTAATTTCTAccagctgaga nd [GEA], [AIBSCS], [BPP] [1]
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
e14 prophage; small regulatory RNA C0293 hcaR repressor 2668895 2668902 AUCACCUU nd [IEP], [SM] [2]


Evidence    

 [TIM] Transcription initiation mapping

 [GEA] Gene expression analysis

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins

 [IEP] Inferred from expression pattern

 [SM] Site mutation


Reference(s)    

 [1] Turlin E., Sismeiro O., Le Caer JP., Labas V., Danchin A., Biville F., 2005, 3-phenylpropionate catabolism and the Escherichia coli oxidative stress response., Res Microbiol 156(3):312-21

 [2] Madikonda AK., Shaikh A., Khanra S., Yakkala H., Yellaboina S., Lin-Chao S., Siddavattam D., 2020, Metabolic remodeling in Escherichia coli MG1655. A prophage e14-encoded small RNA, co293, post-transcriptionally regulates transcription factors HcaR and FadR., FEBS J 287(21):4767-4782

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