RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: uspE
Gene(s): uspE   Genome Browser M3D Gene expression COLOMBOS
Note(s): uspE gene expression is induced under exposure to hydrogen peroxide Hodges AP,2010
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: uspEp
+1: 1398659
Distance from start of the gene: 37
Sequence: ttgatctggcagaaggttcatcactgtttcattcaccagatatgggttaatcttttaattAcaaactgcgttgacagttgt
Evidence: [CV(RS-EPT-CBR)]
[HTIM]
[RS-EPT-CBR]
Reference(s): [1] Mendoza-Vargas A., et al., 2009
[2] Salgado H, et al., 2012
TF binding sites (TFBSs)
[GadX,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd GadX1 activator uspEp nd nd nd nd nd [GEA] [3]
Note(s): 1UspE regulates positively the transcription of the gadX gene in an unknown way, and GadX induces the transcription of uspE Hodges AP,20101UspE regulates positively the transcription of the gadX gene in an unknown way, and GadX induces the transcription of uspE Hodges AP,2010
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation uspEp   [IEP] [4]
Evidence: [IEP] Inferred from expression pattern
Reference(s): [4] Gustavsson N., et al., 2002


Evidence    

 [CV(RS-EPT-CBR)] cross validation(RS-EPT-CBR)

 [HTIM] High-throughput transcription initiation mapping

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [GEA] Gene expression analysis


Reference(s)    

 [1] Mendoza-Vargas A., Olvera L., Olvera M., Grande R., Vega-Alvarado L., Taboada B., Jimenez-Jacinto V., Salgado H., Juarez K., Contreras-Moreira B., Huerta AM., Collado-Vides J., Morett E., 2009, Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli., PLoS One 4(10):e7526

 [2] 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.

 [3] Hodges AP., Dai D., Xiang Z., Woolf P., Xi C., He Y., 2010, Bayesian Network Expansion Identifies New ROS and Biofilm Regulators., PLoS One 5(3):e9513

 [4] Gustavsson N., Diez A., Nystrom T., 2002, The universal stress protein paralogues of Escherichia coli are co-ordinately regulated and co-operate in the defence against DNA damage., Mol Microbiol 43(1):107-17

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