RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: csrB
Gene(s): csrB   Genome Browser M3D Gene expression COLOMBOS
Note(s): Based on gene expression analysis, Jonas K,2006determined that the csrB and csrC genes are under positive control of YhdA. However, they did not show direct evidence for YhdA binding to the crsBp and csrCp promoters.
Although there are two potential binding sites for CRP, CRP1 (ttgTGAGAgatctcTTACAgac) and CRP2 (ctcGGTGTgtaatcTCTCCggt), on the regulatory regions of the csrB gene, it was found that CRP binds nonspecifically on these sites, negatively affecting csrB transcription in an indirect way Pannuri A,2016
Based on microarray and RT-qPCR analyses, it was determined that the csrB gene is downregulated upon exposure to glutathione (GSH) Goswami M,2018
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Liu MY., et al., 1997
Promoter
Name: csrBp
+1: 2924524
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 0
Sequence: ccttaaggcattgtctgtaagcgccttgtaagacttcgcgaaaaagacgattctatcttcGtcgacagggagtcagacaac
                            -35                       -10   +1                   
Evidence: [CV(RS-EPT-CBR/TA)]
[CV(TA/TIM)]
[HTIM]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Gudapaty S., et al., 2001
[3] Mendoza-Vargas A., et al., 2009
[4] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: aataaaaaaaGGGAGCACTGTATTCACAGCGCTCCCggttcgtttc
Reference(s): [1] Liu MY., et al., 1997
TF binding sites (TFBSs)
[IHF,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote IHF activator csrBp 2924617 2924629 -99.0 tttcatttaaAATCAAAATGTTGattgttaatt nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [5]
[UvrY,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote UvrY-Phosphorylated activator csrBp 2924698 2924716 -183.0 ccccatctggTTGTGAGAGATCTCTTACAgactctgtag nd [BPP], [GEA] [5]


Evidence    

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

 [CV(TA/TIM)] cross validation(TA/TIM)

 [HTIM] High-throughput transcription initiation mapping

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

 [TIM] Transcription initiation mapping

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [CV(GEA/ROMA)] cross validation(GEA/ROMA)

 [GEA] Gene expression analysis

 [BPP] Binding of purified proteins


Reference(s)    

 [1] Liu MY., Gui G., Wei B., Preston JF., Oakford L., Yuksel U., Giedroc DP., Romeo T., 1997, The RNA molecule CsrB binds to the global regulatory protein CsrA and antagonizes its activity in Escherichia coli., J Biol Chem 272(28):17502-10

 [2] Gudapaty S., Suzuki K., Wang X., Babitzke P., Romeo T., 2001, Regulatory interactions of Csr components: the RNA binding protein CsrA activates csrB transcription in Escherichia coli., J Bacteriol 183(20):6017-27

 [3] 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

 [4] 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.

 [5] Zere TR., Vakulskas CA., Leng Y., Pannuri A., Potts AH., Dias R., Tang D., Kolaczkowski B., Georgellis D., Ahmer BM., Romeo T., 2015, Genomic Targets and Features of BarA-UvrY (-SirA) Signal Transduction Systems., PLoS One 10(12):e0145035

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