RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: ubiCA
Gene(s): ubiC, ubiA   Genome Browser M3D Gene expression COLOMBOS
Note(s): UbiCA operon expression is high under aerobiosis in the presence of glycerol and electron acceptors. Quinones and menaquinones also induce its expression, but glucose and Casamino acids repress it Kwon O,2005
Soballe B,1997reported that the ubiCA operon is regulated by FNR, and they identified an FNR-binding site; nevertheless Salmon KA,2005 and Kwon O,2005concluded that there is no site for FNR and that an FNR mutant does not cause an effect on the expression of the ubiCA operon.
Reference(s): [1] Heide L., et al., 1993
[2] Nichols BP., et al., 1992
Promoter
Name: ubiCp
+1: 4252443
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 63
Sequence: ttttaccacttcatgcgattgttgcgtttttgttgcgtattagatcacttaatttgctttAcatctcccgtaaacactttt
                            -35                   -10       +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
Reference(s): [3] Huerta AM., et al., 2003
[4] Soballe B., et al., 1997
TF binding sites (TFBSs)
[ArcA,-] 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
nd ArcA-phosphorylated repressor ubiCp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [5]
[FNR,-] 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 FNR repressor ubiCp 4252436 4252449 -0.5 atcacttaatTTGCTTTACATCTCccgtaaacac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [4]
[IHF,-] 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 IHF repressor ubiCp 4252425 4252437 -12.0 ttgcgtattaGATCACTTAATTTgctttacatc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [4]
[NarL,-] 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
nd NarL-phosphorylated repressor ubiCp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [5]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [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.


Reference(s)    

 [1] Heide L., Melzer M., Siebert M., Bechthold A., Schroder J., Severin K., 1993, Clarification of the Escherichia coli genetic map in the 92-minute region containing the ubiCA operon and the plsB, dgk, lexA, and dinF genes., J Bacteriol 175(17):5728-9

 [2] Nichols BP., Green JM., 1992, Cloning and sequencing of Escherichia coli ubiC and purification of chorismate lyase., J Bacteriol 174(16):5309-16

 [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] Soballe B., Poole RK., 1997, Aerobic and anaerobic regulation of the ubiCA operon, encoding enzymes for the first two committed steps of ubiquinone biosynthesis in Escherichia coli., FEBS Lett 414(2):373-6

 [5] Kwon O., Druce-Hoffman M., Meganathan R., 2005, Regulation of the ubiquinone (coenzyme Q) biosynthetic genes ubiCA in Escherichia coli., Curr Microbiol 50(4):180-9

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