RegulonDB RegulonDB 10.7: Operon Form
   

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




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


Transcription unit          
Name: ribA
Gene(s): ribA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Koh YS., et al., 1996
[2] Richter G., et al., 1993
Promoter
Name: ribAp1
+1: 1339190
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 30
Sequence: cgtgaacgatcgacgcgtcgtgattaggtgaaccccttctcgttatggcaaaataagccaAtacagaaccagcattatctg
                        -35                      -10        +1                   
Evidence: [HIPP]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Koh YS., et al., 1996
[3] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: agtaacaactATTTGCTTGCCGGTTATTTTGCTTCCGGCAAGCAAATgaattacaca
Reference(s): [2] Richter G., et al., 1993
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 SoxS activator ribAp1 1339249 1339268 -69.0 aggaaaaattGACAGATTTGTGCCATTCCGtgaacgatcg nd [APIORCISFBSCS], [BPP], , [GEA], [IHBCE], [1], [4], [5], [6]


Transcription unit       
Name: ribA
Gene(s): ribA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Koh YS., et al., 1996
[2] Richter G., et al., 1993
Promoter
Name: ribAp2
+1: 1339234
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 74
Sequence: tgaaaacgccagttccaggaaaaattgacagatttgtgccattccgtgaacgatcgacgcGtcgtgattaggtgaacccct
                         -35                     -10        +1                   
Evidence: [HIPP]
[TIM]
Reference(s): [1] Koh YS., et al., 1996
Terminator(s)
Type: rho-independent
Sequence: agtaacaactATTTGCTTGCCGGTTATTTTGCTTCCGGCAAGCAAATgaattacaca
Reference(s): [2] Richter G., et al., 1993




Reference(s)    

 [1] Koh YS., Choih J., Lee JH., Roe JH., 1996, Regulation of the ribA gene encoding GTP cyclohydrolase II by the soxRS locus in Escherichia coli., Mol Gen Genet 251(5):591-8

 [2] Richter G., Ritz H., Katzenmeier G., Volk R., Kohnle A., Lottspeich F., Allendorf D., Bacher A., 1993, Biosynthesis of riboflavin: cloning, sequencing, mapping, and expression of the gene coding for GTP cyclohydrolase II in Escherichia coli., J Bacteriol 175(13):4045-51

 [3] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [4] Koh YS., Chung WH., Lee JH., Roe JH., 1999, The reversed SoxS-binding site upstream of the ribA promoter in Escherichia coli., Mol Gen Genet 261(2):374-80

 [5] Martin RG., Gillette WK., Rhee S., Rosner JL., 1999, Structural requirements for marbox function in transcriptional activation of mar/sox/rob regulon promoters in Escherichia coli: sequence, orientation and spatial relationship to the core promoter., Mol Microbiol 34(3):431-41

 [6] Seo SW., Kim D., Szubin R., Palsson BO., 2015, Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655., Cell Rep 12(8):1289-99


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