RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: pfkA
Gene(s): pfkA   Genome Browser M3D Gene expression COLOMBOS
Note(s): Under nitrogen-rich growth conditions, the expression of the pfkA gene was increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, it is unknown if the effects of the transcriptional regulators act directly on gene expression; also, it is unknown which of the two promoters that transcribe the gene could be regulated by the regulators Kumar R,2011
The expression of the gene pfkA is increased under acidic growth conditions in aerobiosis but not in microaerobiosis Marzan LW,2013 The increased expression of this gene is in agreement with the increased specific glucose consumption rate observed under acidic conditions Marzan LW,2013
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: pfkAp2
+1: 4107474
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 78
Sequence: accgccatttggcctgacctgaatcaattcagcaggaagtgattgttatactatttgcacAttcgttggatcacttcgatg
                                              -10           +1                   
Evidence: [HIPP]
[HTTIM]
[RS-EPT-CBR]
Reference(s): [1] Crooke H., et al., 1995
[2] Hellinga HW., et al., 1985
[3] Mendoza-Vargas A., et al., 2009
[4] Olvera L., et al., 2009
[5] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: catggacaaaGCGCACTTTGTCAGCAATATGAGGCGGATTTCTTCCGCCTTTTTAATCCCTCAACatatacccgc
Reference(s): [6] Feng CQ., et al., 2019
[7] Lesnik EA., et al., 2001
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
proximal Cra1 repressor pfkAp2 4107430 4107447 -35.5 atttggcctgACCTGAATCAATTCAGCAGgaagtgattg nd [BPP] [8]
Note(s): 1The FruR site in the pfkA gene overlaps with the -35 box, so it is proposed that FruR inhibits pfkA transcription, avoiding the RNA polymerase access to its binding site.1The FruR site in the pfkA gene overlaps with the -35 box, so it is proposed that FruR inhibits pfkA transcription, avoiding the RNA polymerase access to its binding site.


Transcription unit          
Name: pfkA
Gene(s): pfkA   Genome Browser M3D Gene expression COLOMBOS
Note(s): Under nitrogen-rich growth conditions, the expression of the pfkA gene was increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, it is unknown if the effects of the transcriptional regulators act directly on gene expression; also, it is unknown which of the two promoters that transcribe the gene could be regulated by the regulators Kumar R,2011
The expression of the gene pfkA is increased under acidic growth conditions in aerobiosis but not in microaerobiosis Marzan LW,2013 The increased expression of this gene is in agreement with the increased specific glucose consumption rate observed under acidic conditions Marzan LW,2013
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: pfkAp
+1: 4107474
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 78
Sequence: accgccatttggcctgacctgaatcaattcagcaggaagtgattgttatactatttgcacAttcgttggatcacttcgatg
                                              -10           +1                   
Evidence: [HIPP]
[HTTIM]
[RS-EPT-CBR]
Reference(s): [1] Crooke H., et al., 1995
[2] Hellinga HW., et al., 1985
[3] Mendoza-Vargas A., et al., 2009
[4] Olvera L., et al., 2009
[5] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: catggacaaaGCGCACTTTGTCAGCAATATGAGGCGGATTTCTTCCGCCTTTTTAATCCCTCAACatatacccgc
Reference(s): [6] Feng CQ., et al., 2019
[7] Lesnik EA., et al., 2001
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
proximal Cra1 repressor pfkAp 4107430 4107447 -35.5 atttggcctgACCTGAATCAATTCAGCAGgaagtgattg nd [BPP] [8]
Note(s): 1The FruR site in the pfkA gene overlaps with the -35 box, so it is proposed that FruR inhibits pfkA transcription, avoiding the RNA polymerase access to its binding site.1The FruR site in the pfkA gene overlaps with the -35 box, so it is proposed that FruR inhibits pfkA transcription, avoiding the RNA polymerase access to its binding site.


Transcription unit       
Name: pfkA
Gene(s): pfkA   Genome Browser M3D Gene expression COLOMBOS
Note(s): Under nitrogen-rich growth conditions, the expression of the pfkA gene was increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, it is unknown if the effects of the transcriptional regulators act directly on gene expression; also, it is unknown which of the two promoters that transcribe the gene could be regulated by the regulators Kumar R,2011
The expression of the gene pfkA is increased under acidic growth conditions in aerobiosis but not in microaerobiosis Marzan LW,2013 The increased expression of this gene is in agreement with the increased specific glucose consumption rate observed under acidic conditions Marzan LW,2013
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: pfkAp3
+1: 4107522
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 30
Sequence: tactatttgcacattcgttggatcacttcgatgtgcaagaagacttccggcaacagatttCattttgcattccaaagttca
                                        -10                 +1                   
Evidence: [HTTIM]
Reference(s): [4] Olvera L., et al., 2009
Terminator(s)
Type: rho-independent
Sequence: catggacaaaGCGCACTTTGTCAGCAATATGAGGCGGATTTCTTCCGCCTTTTTAATCCCTCAACatatacccgc
Reference(s): [6] Feng CQ., et al., 2019
[7] Lesnik EA., et al., 2001


Transcription unit       
Name: pfkA
Gene(s): pfkA   Genome Browser M3D Gene expression COLOMBOS
Note(s): Under nitrogen-rich growth conditions, the expression of the pfkA gene was increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, it is unknown if the effects of the transcriptional regulators act directly on gene expression; also, it is unknown which of the two promoters that transcribe the gene could be regulated by the regulators Kumar R,2011
The expression of the gene pfkA is increased under acidic growth conditions in aerobiosis but not in microaerobiosis Marzan LW,2013 The increased expression of this gene is in agreement with the increased specific glucose consumption rate observed under acidic conditions Marzan LW,2013
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: pfkAp1
+1: 4107522
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 30
Sequence: tactatttgcacattcgttggatcacttcgatgtgcaagaagacttccggcaacagatttCattttgcattccaaagttca
                                        -10                 +1                   
Evidence: [HTTIM]
Reference(s): [4] Olvera L., et al., 2009
Terminator(s)
Type: rho-independent
Sequence: catggacaaaGCGCACTTTGTCAGCAATATGAGGCGGATTTCTTCCGCCTTTTTAATCCCTCAACatatacccgc
Reference(s): [6] Feng CQ., et al., 2019
[7] Lesnik EA., et al., 2001




Reference(s)    

 [1] Crooke H., Cole J., 1995, The biogenesis of c-type cytochromes in Escherichia coli requires a membrane-bound protein, DipZ, with a protein disulphide isomerase-like domain., Mol Microbiol 15(6):1139-50

 [2] Hellinga HW., Evans PR., 1985, Nucleotide sequence and high-level expression of the major Escherichia coli phosphofructokinase., Eur J Biochem 149(2):363-73

 [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] Olvera L., Mendoza-Vargas A., Flores N., Olvera M., Sigala JC., Gosset G., Morett E., Bolivar F., 2009, Transcription analysis of central metabolism genes in Escherichia coli. Possible roles of sigma38 in their expression, as a response to carbon limitation., PLoS One 4(10):e7466

 [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] Feng CQ., Zhang ZY., Zhu XJ., Lin Y., Chen W., Tang H., Lin H., 2019, iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators., Bioinformatics 35(9):1469-1477

 [7] Lesnik EA., Sampath R., Levene HB., Henderson TJ., McNeil JA., Ecker DJ., 2001, Prediction of rho-independent transcriptional terminators in Escherichia coli., Nucleic Acids Res 29(17):3583-94

 [8] Negre D., Bonod-Bidaud C., Geourjon C., Deleage G., Cozzone AJ., Cortay JC., 1996, Definition of a consensus DNA-binding site for the Escherichia coli pleiotropic regulatory protein, FruR., Mol Microbiol 21(2):257-66


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