RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit       
Name: cfa
Synonym(s): cdfA
Gene(s): cfa   Genome Browser M3D Gene expression COLOMBOS
Note(s): Both promoters cfap2 (σ38) and cfap1 (σ38 and σ70) are induced in response to neutral acetate Rosenthal AZ,2006. Rosenthal AZ,2008 and they do not need accessory elements (activators or repressors), which suggests that acetate works directly with RNA polymerase in the transcription complex. The general responses to acetate of the two RNA polymerase forms were clearly different; σ70 promoters responded with wide differences, but σ38 promoters were generally activated Rosenthal AZ,2008
cfa transcription is also induced by acidic and osmotic stress Arnold CN, McElhanon J, Lee A, Leonhart R, Siegele DA,2001. Weber H,2005 cfap1 contains a perfect 14-bp inverted repeat with two half-site elements that read 5'-TTTTGTT-3', centered at position -40. No information concerning this inverted repeat is available, since it does not align with any known regulator-binding sites Rosenthal AZ,2008
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Wang AY., et al., 1994
Promoter
Name: cfap1
+1: 1741201
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 212
Sequence: tacttaggctgctaacaaaattttgttgtatgattgaaattagcggcctatactaatttcGagttgttaaagctacgataa
                          -35                    -10        +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
[RS-EPT-CBR]
Reference(s): [2] Huerta AM., et al., 2003
[3] Kvint K., et al., 2000
[4] Rosenthal AZ., et al., 2008
[5] Salgado H, et al., 2012
[1] Wang AY., et al., 1994
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA CpxQ cfa repressor 1741278 1741285 GGCAAGGG MRNA-DEGRADATION [EXP-IEP], [EXP-IMP-SITE-MUTATION], [EXP-IPI] [6]
small regulatory RNA RydC cfa activator 1741304 1741314 UCUACGUCGGA MRNA-DEGRADATION [COMP], [EXP-IEP], [EXP-IMP-SITE-MUTATION], [EXP-IPI] [6], [7]
small regulatory RNA ArrS cfa activator 1741309 1741318 GUCGGAUUAU nd [EXP-IEP], [EXP-IMP-SITE-MUTATION], [EXP-IPI] [6]


Transcription unit       
Name: cfa
Synonym(s): cdfA
Gene(s): cfa   Genome Browser M3D Gene expression COLOMBOS
Note(s): Both promoters cfap2 (σ38) and cfap1 (σ38 and σ70) are induced in response to neutral acetate Rosenthal AZ,2006. Rosenthal AZ,2008 and they do not need accessory elements (activators or repressors), which suggests that acetate works directly with RNA polymerase in the transcription complex. The general responses to acetate of the two RNA polymerase forms were clearly different; σ70 promoters responded with wide differences, but σ38 promoters were generally activated Rosenthal AZ,2008
cfa transcription is also induced by acidic and osmotic stress Arnold CN, McElhanon J, Lee A, Leonhart R, Siegele DA,2001. Weber H,2005 cfap1 contains a perfect 14-bp inverted repeat with two half-site elements that read 5'-TTTTGTT-3', centered at position -40. No information concerning this inverted repeat is available, since it does not align with any known regulator-binding sites Rosenthal AZ,2008
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Wang AY., et al., 1994
Promoter
Name: cfap
+1: 1741201
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 212
Sequence: tacttaggctgctaacaaaattttgttgtatgattgaaattagcggcctatactaatttcGagttgttaaagctacgataa
                         -35                -10             +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
[RS-EPT-CBR]
Reference(s): [2] Huerta AM., et al., 2003
[3] Kvint K., et al., 2000
[4] Rosenthal AZ., et al., 2008
[5] Salgado H, et al., 2012
[1] Wang AY., et al., 1994
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA RydC cfa activator 1741304 1741314 UCUACGUCGGA MRNA-DEGRADATION [COMP], [EXP-IEP], [EXP-IMP-SITE-MUTATION], [EXP-IPI] [6], [7]
small regulatory RNA ArrS cfa activator 1741309 1741318 GUCGGAUUAU nd [EXP-IEP], [EXP-IMP-SITE-MUTATION], [EXP-IPI] [6]
small regulatory RNA CpxQ cfa repressor 1741278 1741285 GGCAAGGG MRNA-DEGRADATION [EXP-IEP], [EXP-IMP-SITE-MUTATION], [EXP-IPI] [6]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation cfap nd   [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [3]
Evidence: [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
Reference(s): [3] Kvint K., et al., 2000


Transcription unit       
Name: cfa
Synonym(s): cdfA
Gene(s): cfa   Genome Browser M3D Gene expression COLOMBOS
Note(s): Both promoters cfap2 (σ38) and cfap1 (σ38 and σ70) are induced in response to neutral acetate Rosenthal AZ,2006. Rosenthal AZ,2008 and they do not need accessory elements (activators or repressors), which suggests that acetate works directly with RNA polymerase in the transcription complex. The general responses to acetate of the two RNA polymerase forms were clearly different; σ70 promoters responded with wide differences, but σ38 promoters were generally activated Rosenthal AZ,2008
cfa transcription is also induced by acidic and osmotic stress Arnold CN, McElhanon J, Lee A, Leonhart R, Siegele DA,2001. Weber H,2005 cfap1 contains a perfect 14-bp inverted repeat with two half-site elements that read 5'-TTTTGTT-3', centered at position -40. No information concerning this inverted repeat is available, since it does not align with any known regulator-binding sites Rosenthal AZ,2008
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Wang AY., et al., 1994
Promoter
Name: cfap2
+1: 1741379
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 34
Sequence: agactcgcggttttttctgcgagatttctcacaaagcccaaaaagcgtctacgctgttttAaggttctgatcaccgaccag
                            -35              -10            +1                   
Note(s): Region 4 of the σ38 protein and the elements near the -35 DNA region are involved in the response to high acetate concentrations, which ensures the transcriptional activation of the cfap2 promoter to counteract these physiological changes Rosenthal AZ,2006.
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[4] Rosenthal AZ., et al., 2008
[1] Wang AY., et al., 1994


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] 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

 [EXP-IMP-SITE-MUTATION] Site mutation

 [EXP-IPI] Inferred from physical interaction

 [COMP] Inferred by computational analysis

 [EXP-IDA] Inferred from direct assay


Reference(s)    

 [1] Wang AY., Cronan JE., 1994, The growth phase-dependent synthesis of cyclopropane fatty acids in Escherichia coli is the result of an RpoS(KatF)-dependent promoter plus enzyme instability., Mol Microbiol 11(6):1009-17

 [2] 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

 [3] Kvint K., Farewell A., Nystrom T., 2000, RpoS-dependent promoters require guanosine tetraphosphate for induction even in the presence of high levels of sigma(s)., J Biol Chem 275(20):14795-8

 [4] Rosenthal AZ., Kim Y., Gralla JD., 2008, Regulation of transcription by acetate in Escherichia coli: in vivo and in vitro comparisons., Mol Microbiol 68(4):907-17

 [5] 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.

 [6] Bianco CM., Frohlich KS., Vanderpool CK., 2019, Bacterial Cyclopropane Fatty Acid Synthase mRNA Is Targeted by Activating and Repressing Small RNAs., J Bacteriol 201(19)

 [7] King AM., Vanderpool CK., Degnan PH., 2019, sRNA Target Prediction Organizing Tool (SPOT) Integrates Computational and Experimental Data To Facilitate Functional Characterization of Bacterial Small RNAs., mSphere 4(1)

RegulonDB