RegulonDB RegulonDB 11.0: 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: [HIPP]
[ICWHO]
[IHBCE]
[IMP]
[IPI]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Huerta AM., et al., 2003
[2] Salgado H, et al., 2012
[3] 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: [HIPP]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Salgado H, et al., 2012
[3] 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: [HIPP]
[HTTIM]    
[ICWHO]
[IEP]
[IHBCE]
[IMP]
[IPI]
[RS-EPT-CBR]
[TIM]
Reference(s): [4] Edwards AN., et al., 2011
[1] Huerta AM., et al., 2003
[5] Mendoza-Vargas A., et al., 2009
[2] Salgado H, et al., 2012
[3] 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]
[ICWHO]
[IHBCE]
[IMP]
[IPI]
[TIM]
Reference(s): [1] Huerta AM., et al., 2003
[3] 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: csrAp
+1: 2819373
Sigma Factor: Sigma38 Sigmulon
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]
[ICWHO]
[IHBCE]
[IMP]
[IPI]
[TIM]
Reference(s): [1] Huerta AM., et al., 2003
[3] 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 Sigmulon
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]
[ICWHO]
[IHBCE]
[IMP]
[IPI]
[TIM]
Reference(s): [1] Huerta AM., et al., 2003
[3] Yakhnin H., et al., 2011




Reference(s)    

 [1] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [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] 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

 [4] Edwards AN., Patterson-Fortin LM., Vakulskas CA., Mercante JW., Potrykus K., Vinella D., Camacho MI., Fields JA., Thompson SA., Georgellis D., Cashel M., Babitzke P., Romeo T., 2011, Circuitry linking the Csr and stringent response global regulatory systems., Mol Microbiol 80(6):1561-80

 [5] 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


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