RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: csrC
Gene(s): csrC   Genome Browser M3D Gene expression COLOMBOS
Note(s): CsrC possesses several of the imperfect repeat sequences that characterize CsrB RNA.
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.
CRP does not repress csrC expression via effects on CsrA or UvrY. However, repression of csrC by CRP acts in conjunction with UvrY-dependent activation. Both transcription factors compete for binding in a region far upstream of csrC Pannuri A,2016
The circuit formed by Csr and the catabolite repression regulatory system for the complex global regulatory system has been determined Pannuri A,2016
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Argaman L., et al., 2001
[2] Weilbacher T., et al., 2003
Promoter
Name: csrCp
+1: 4051036
Distance from start of the gene: 0
Sequence: atgtgcaaatactgatggcggttgattgtttgtttaaagcaaaggcgtaaagtagcacccAtagagcgaggacgctaacag
Evidence: [RS-EPT-CBR]
[TIM]
Reference(s): [1] Argaman L., et al., 2001
[3] Salgado H, et al., 2012
[2] Weilbacher T., et al., 2003
Terminator(s)
Type: rho-independent
Sequence: gttatgagtcAGGAAAAAAGGCGACAGAGTAATCTGTCGCCTTTTTTCTTtgcttgcttt
Reference(s): [2] Weilbacher T., et al., 2003
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
remote CRP-cAMP1 repressor csrCp 4050837 4050853 -191.5 gatttttcggCGTGAGCGTTGTAAGTAaaagccatac nd [APIORCISFBSCS], [BPP], [GEA] [4]
remote CRP-cAMP2 repressor csrCp 4050868 4050884 -160.5 ccatacgcttTGTGAGACATTGCCGATagtctttatg nd [APIORCISFBSCS], [BPP], [GEA] [4]
remote CRP-cAMP3 repressor csrCp 4050915 4050931 -113.5 gagaaaattcTGCGATGCATGTCAAATaagctatata nd [APIORCISFBSCS], [BPP], [GEA] [4]
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 csrCp 4050868 4050886 -159.0 ccatacgcttTGTGAGACATTGCCGATAGtctttatgcg nd [BPP], [GEA] [5]
Note(s): 1This site (-191.5) is called RIII Pannuri A,2016
2This site (-160.5) is called RII Pannuri A,2016
3The RI site (-113.5) has the highest affinity, since protection occurred at a low concentration of CRP (50 nM) Pannuri A,20161This site (-191.5) is called RIII Pannuri A,2016
2This site (-160.5) is called RII Pannuri A,2016
4The RI site (-113.5) has the highest affinity, since protection occurred at a low concentration of CRP (50 nM) Pannuri A,2016




Reference(s)    

 [1] Argaman L., Hershberg R., Vogel J., Bejerano G., Wagner EG., Margalit H., Altuvia S., 2001, Novel small RNA-encoding genes in the intergenic regions of Escherichia coli., Curr Biol 11(12):941-50

 [2] Weilbacher T., Suzuki K., Dubey AK., Wang X., Gudapaty S., Morozov I., Baker CS., Georgellis D., Babitzke P., Romeo T., 2003, A novel sRNA component of the carbon storage regulatory system of Escherichia coli., Mol Microbiol 48(3):657-70

 [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] Pannuri A., Vakulskas CA., Zere T., McGibbon LC., Edwards AN., Georgellis D., Babitzke P., Romeo T., 2016, Circuitry Linking the Catabolite Repression and Csr Global Regulatory Systems of Escherichia coli., J Bacteriol 198(21):3000-3015

 [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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