RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: pykF
Gene(s): pykF   Genome Browser M3D Gene expression COLOMBOS
Note(s): There is no evidence in the literature of pykF forming a transcription unit with the upstream lpp gene, which is in the same orientation but 311 bp upstream, and the downstream gene is oriented in the opposite direction. So, the pykF gene is defined as an isolated gene.
Under nitrogen-rich growth conditions, the expression of the pykF gene 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, under nitrogen-limited growth conditions, gene expression was decreased in the Fnr mutant. It is unknown if the effects of the transcriptional regulators act directly on gene expression; also, it is unknown which of the four promoters that transcribe the gene could be regulated by the regulators Kumar R,2011
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Bledig SA., et al., 1996
Promoter
Name: pykFp
+1: 1755467
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 231
Sequence: atattttttgaaacgctgtttttgttttccttttggattaatttcagcgtataatgcgcgCcaattgactcttgaatggtt
                          -35                     -10       +1                   
Note(s): Although the evidence for the promoter is only sequence similarity, a mutation at the cis-site for the binding of FruR clearly shows repression of activity of pykF gene 7559366.
Evidence: [HIPP]
[ICWHO]
Reference(s): [1] Bledig SA., et al., 1996
[2] Huerta AM., 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
proximal Cra1 repressor pykFp 1755476 1755493 18.5 gccaattgacTCTTGAATGGTTTCAGCACtttggactgt nd [BCE], [SM] [1]
Note(s): 1The FruR effect for pykF was tested in the presence of different glycolytic and gluconeogenic substrates. It was found that FruR binds to its control region, downstream of the putative promoter, to repress it during gluconeogenesis. During glycolysis, when fructose or fructose-1,6-diphosphate is available, FruR unbinds the pykF site Bledig SA,1996.1The FruR effect for pykF was tested in the presence of different glycolytic and gluconeogenic substrates. It was found that FruR binds to its control region, downstream of the putative promoter, to repress it during gluconeogenesis. During glycolysis, when fructose or fructose-1,6-diphosphate is available, FruR unbinds the pykF site Bledig SA,1996.


Transcription unit       
Name: pykF
Gene(s): pykF   Genome Browser M3D Gene expression COLOMBOS
Note(s): Under nitrogen-rich growth conditions, the expression of the pykF gene 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, under nitrogen-limited growth conditions, gene expression was decreased in the Fnr mutant. It is unknown if the effects of the transcriptional regulators act directly on gene expression; also, it is unknown which of the four promoters that transcribe the gene could be regulated by the regulators Kumar R,2011
Evidence: [IC] Inferred by curator
Promoter
Name: pykFp4
+1: 1755600
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 98
Sequence: ggctgagacacaagcacacattcctctgcacgctttttcgatgtcacctatccttagagcGaggcaccaccactttcgtaa
                                                -10         +1                   
Evidence: [HTTIM]
[RS-EPT-CBR]
Reference(s): [3] Mendoza-Vargas A., et al., 2009
[4] Olvera L., et al., 2009
[5] Salgado H, et al., 2012


Transcription unit       
Name: pykF
Gene(s): pykF   Genome Browser M3D Gene expression COLOMBOS
Note(s): Under nitrogen-rich growth conditions, the expression of the pykF gene 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, under nitrogen-limited growth conditions, gene expression was decreased in the Fnr mutant. It is unknown if the effects of the transcriptional regulators act directly on gene expression; also, it is unknown which of the four promoters that transcribe the gene could be regulated by the regulators Kumar R,2011
Evidence: [IC] Inferred by curator
Promoter
Name: pykFp2
+1: 1755600
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 98
Sequence: ggctgagacacaagcacacattcctctgcacgctttttcgatgtcacctatccttagagcGaggcaccaccactttcgtaa
                                                -10         +1                   
Evidence: [HTTIM]
[RS-EPT-CBR]
Reference(s): [3] Mendoza-Vargas A., et al., 2009
[4] Olvera L., et al., 2009
[5] Salgado H, et al., 2012


Transcription unit       
Name: pykF
Gene(s): pykF   Genome Browser M3D Gene expression COLOMBOS
Note(s): Under nitrogen-rich growth conditions, the expression of the pykF gene 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, under nitrogen-limited growth conditions, gene expression was decreased in the Fnr mutant. It is unknown if the effects of the transcriptional regulators act directly on gene expression; also, it is unknown which of the four promoters that transcribe the gene could be regulated by the regulators Kumar R,2011
Evidence: [IC] Inferred by curator
Promoter
Name: pykFp3
+1: 1755617
Distance from start of the gene: 81
Sequence: acattcctctgcacgctttttcgatgtcacctatccttagagcgaggcaccaccactttcGtaataccggattcgctttcc
Evidence: [HTTIM]
Reference(s): [4] Olvera L., et al., 2009


Transcription unit       
Name: pykF
Gene(s): pykF   Genome Browser M3D Gene expression COLOMBOS
Note(s): Under nitrogen-rich growth conditions, the expression of the pykF gene 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, under nitrogen-limited growth conditions, gene expression was decreased in the Fnr mutant. It is unknown if the effects of the transcriptional regulators act directly on gene expression; also, it is unknown which of the four promoters that transcribe the gene could be regulated by the regulators Kumar R,2011
Evidence: [IC] Inferred by curator
Promoter
Name: pykFp5
+1: 1755663
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 35
Sequence: gcaccaccactttcgtaataccggattcgctttccggcagtgcgcccagaaagcaagtttCtcccatccttctcaacttaa
                                              -10           +1                   
Evidence: [HTTIM]
Reference(s): [3] Mendoza-Vargas A., et al., 2009
[4] Olvera L., et al., 2009


Transcription unit       
Name: pykF
Gene(s): pykF   Genome Browser M3D Gene expression COLOMBOS
Note(s): Under nitrogen-rich growth conditions, the expression of the pykF gene 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, under nitrogen-limited growth conditions, gene expression was decreased in the Fnr mutant. It is unknown if the effects of the transcriptional regulators act directly on gene expression; also, it is unknown which of the four promoters that transcribe the gene could be regulated by the regulators Kumar R,2011
Evidence: [IC] Inferred by curator
Promoter
Name: pykFp1
+1: 1755663
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 35
Sequence: gcaccaccactttcgtaataccggattcgctttccggcagtgcgcccagaaagcaagtttCtcccatccttctcaacttaa
                                              -10           +1                   
Evidence: [HTTIM]
Reference(s): [3] Mendoza-Vargas A., et al., 2009
[4] Olvera L., et al., 2009




Reference(s)    

 [1] Bledig SA., Ramseier TM., Saier MH., 1996, Frur mediates catabolite activation of pyruvate kinase (pykF) gene expression in Escherichia coli., J Bacteriol 178(1):280-3

 [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] 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.


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