RegulonDB RegulonDB 11.1: Operon Form
   

wrbA-yccJ operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: wrbA-yccJ
Gene(s): yccJ, wrbA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The wrbA gene is upregulated by long-term (8 to 12 h) exposure of E. coli to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020.
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: wrbAp
+1: 1067758
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 50
Sequence: ataaatcaaataagtggttgtgaaatttgcactctgaaaaggacgtcttatctttaaataAgtggtagcgaatcgctacgg
                                -35                    -10  +1                   
Evidence: [COMP-HINF]
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
[EXP-IEP]
[RS-EPT-CBR]
Reference(s): [1] Dudin O., et al., 2013
[2] Mendoza-Vargas A., et al., 2009
[3] Salgado H, et al., 2012
TF binding sites (TFBSs)
[CsgD,+] 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
remote CsgD activator wrbAp 1067866 1067880 -114.5 tatgattaaaAAAACGCGATGAGATaaaaatgtgt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [4]
remote CsgD activator wrbAp 1067888 1067902 -136.5 ataattatccATAAGCCGCTCTTATgattaaaaaa nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [4]
remote CsgD activator wrbAp 1067918 1067932 -166.5 gcttcttagcGAGAATAGATATCATctccaataat nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [4]


Evidence    

 [COMP-HINF] Inferred by a human based on computational evidence

 [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] High-throughput transcription initiation mapping

 [EXP-IEP] Inferred from expression pattern

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

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins


Reference(s)    

 [1] Dudin O., Lacour S., Geiselmann J., 2013, Expression dynamics of RpoS/Crl-dependent genes in Escherichia coli., Res Microbiol 164(8):838-47

 [2] 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

 [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] Ogasawara H., Yamamoto K., Ishihama A., 2011, Role of the biofilm master regulator CsgD in cross-regulation between biofilm formation and flagellar synthesis., J Bacteriol 193(10):2587-97

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