RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit       
Name: csrA
Gene(s): csrA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: csrAp5
+1: 2819189
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 43
Sequence: ttagatgtaatgtgtttgtcattgcttactttttggcgttatatgatggataatgccgggAtacagagagacccgactctt
                      -35                        -10        +1                   
Note(s): The csrAp5 is promoter is expressed during the transition from exponential to stationary phases Yakhnin H,2011
Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[HIPP]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Salgado H, et al., 2012
[2] Yakhnin H., et al., 2011


Transcription unit       
Name: csrA
Gene(s): csrA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: csrAp4
+1: 2819198
Distance from start of the gene: 52
Sequence:
Note(s): The csrAp4 promoter was identified by in vivo but not by in vitro experiments Yakhnin H,2011
Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[HIPP]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Salgado H, et al., 2012
[2] Yakhnin H., et al., 2011


Transcription unit       
Gene(s): csrA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: csrAp3
+1: 2819273
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 127
Sequence: aacgctatcgacaacgataaagtcaggttgaagttgtgtatatcggctaaacttaggtttAacagaatgtaatgccatgac
                        -35                -10              +1                   
Note(s): The csrAp3 promoter is highly expressed during the transition from exponential to stationary phase. This promoter is a strong σS-dependent promoter that is also activated by σ70. The protein CsrA appears to indirectly induce transcription of the csrA gene from the csrAp3 promoter Yakhnin H,2011
Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[HIPP]
[HTIM]
[RS-EPT-CBR]
[TIM]
Reference(s): [3] Mendoza-Vargas A., et al., 2009
[1] Salgado H, et al., 2012
[2] Yakhnin H., et al., 2011


Transcription unit       
Name: csrA
Gene(s): csrA   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: csrAp2
+1: 2819370
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 224
Sequence: ctgcagcgttagccagtgtgaaaggctgggtcagcgcgaaattgcaataatataagcgtcAggcaatgccgtggactcgct
                          -35                   -10         +1                   
Note(s): The csrAp2 promoter, which overlaps with the csrAp1 promoter, is a weak promoter whose activity is dependent on σ70 Yakhnin H,2011
Evidence: [HIPP]
[TIM]
Reference(s): [2] Yakhnin H., et al., 2011


Transcription unit       
Name: csrA
Gene(s): csrA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: csrAp1
+1: 2819373
Sigma Factor: Sigma70, Sigma38
Distance from start of the gene: 227
Sequence: tacctgcagcgttagccagtgtgaaaggctgggtcagcgcgaaattgcaataatataagcGtcaggcaatgccgtggactc
                         -35                -10             +1                   
Note(s): The csrAp1 promoter, which overlaps with the csrAp2 promoter, is a weak promoter that is activated by both σ70 and σS Yakhnin H,2011
Evidence: [HIPP]
[TIM]
Reference(s): [2] Yakhnin H., et al., 2011


Regulation by sRNA    
  Small RNA name (Regulator) Regulation type Mechanism Function Binding Sites Evidence Reference
LeftPos RightPos Sequence (RNA-strand)
  csrC antagonist post-translational regulation repressor       [GEA]
[IPI]
[4]
Notes: "The provided sequence is that of the RNA strand,i.e. 'U's are showed instead the 'T'"




Reference(s)    

 [1] 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.

 [2] Yakhnin H., Yakhnin AV., Baker CS., Sineva E., Berezin I., Romeo T., Babitzke P., 2011, Complex regulation of the global regulatory gene csrA: CsrA-mediated translational repression, transcription from five promoters by Eσ(70) and Eσ(S) , and indirect transcriptional activation by CsrA., Mol Microbiol 81(3):689-704

 [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] 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


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