RegulonDB RegulonDB 10.10: Operon Form
   

focA-pflB operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: pflB
Gene(s): pflB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Sawers G., et al., 1989
Promoter
Name: pflBp1
+1: 953579
Distance from start of the gene: 25
Sequence: catttacctgcgtgaaaacgaccaccattaatggttgtcgaagtacgcagtaaataaaaaAtccacttaagaaggtaggtg
Evidence: [HIPP]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Salgado H, et al., 2012
[1] Sawers G., et al., 1989
Terminator(s)
Type: rho-independent
Sequence: tcgcgctaaaAAAGGCCCCACTTTCGTGGAGCCTTTATTGTACGCTTTTTACTGTACGATTTCAGTCAAAtctaattaca
Note(s): This terminator presents a double stem-loop structure.
Reference(s): [1] Sawers G., et al., 1989
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 Fis repressor pflBp1 953574 953588 -2.0 agtacgcagtAAATAAAAAATCCACttaagaaggt nd [GEA], [AIBSCS] [3]


Transcription unit       
Name: pflB
Gene(s): pflB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Sawers G., et al., 1989
Promoter
Name: pflBp2
+1: 953641
Distance from start of the gene: 87
Sequence: attccggttacgatcggcaacattatcggtggtggtttgttggttgggttgacatactggGtcatttacctgcgtgaaaac
Evidence: [HIPP]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Salgado H, et al., 2012
[1] Sawers G., et al., 1989
Terminator(s)
Type: rho-independent
Sequence: tcgcgctaaaAAAGGCCCCACTTTCGTGGAGCCTTTATTGTACGCTTTTTACTGTACGATTTCAGTCAAAtctaattaca
Note(s): This terminator presents a double stem-loop structure.
Reference(s): [1] Sawers G., et al., 1989


Transcription unit       
Name: pflB
Gene(s): pflB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Sawers G., et al., 1989
Promoter
Name: pflBp3
+1: 953741
Distance from start of the gene: 187
Sequence: aatccgcgacttcgcatccccggaattttggaccgcagtcggttctgcaccggaaaatttTtctcacctgaccgtgatgaa
Evidence: [HIPP]
[TIM]
Reference(s): [1] Sawers G., et al., 1989
Terminator(s)
Type: rho-independent
Sequence: tcgcgctaaaAAAGGCCCCACTTTCGTGGAGCCTTTATTGTACGCTTTTTACTGTACGATTTCAGTCAAAtctaattaca
Note(s): This terminator presents a double stem-loop structure.
Reference(s): [1] Sawers G., et al., 1989


Transcription unit       
Name: pflB
Gene(s): pflB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Sawers G., et al., 1989
Promoter
Name: pflBp4
+1: 953851
Distance from start of the gene: 297
Sequence: cgcagcctgatggacaaagcgttcattatggtgctgccggtcgcgatgtttgttgccagcGgttttgagcacagtatcgca
Evidence: [HIPP]
[TIM]
Reference(s): [1] Sawers G., et al., 1989
Terminator(s)
Type: rho-independent
Sequence: tcgcgctaaaAAAGGCCCCACTTTCGTGGAGCCTTTATTGTACGCTTTTTACTGTACGATTTCAGTCAAAtctaattaca
Note(s): This terminator presents a double stem-loop structure.
Reference(s): [1] Sawers G., et al., 1989


Transcription unit       
Name: pflB
Gene(s): pflB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Sawers G., et al., 1989
Promoter
Name: pflBp5
+1: 953925
Distance from start of the gene: 371
Sequence: ttattgaggccgtctgtcttggtatcctggcaaacctgatggtatgtctggcagtatggaTgagttattctggccgcagcc
Evidence: [HIPP]
[TIM]
Reference(s): [1] Sawers G., et al., 1989
Terminator(s)
Type: rho-independent
Sequence: tcgcgctaaaAAAGGCCCCACTTTCGTGGAGCCTTTATTGTACGCTTTTTACTGTACGATTTCAGTCAAAtctaattaca
Note(s): This terminator presents a double stem-loop structure.
Reference(s): [1] Sawers G., et al., 1989


Transcription unit          
Name: focA-pflB
Synonym(s): pfl
Gene(s): pflB, focA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The focA gene and pflB gene are cotranscribed, but pflB is also transcribed alone.
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for focA . This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Sawers G., et al., 1989
Promoter
Name: focAp1
+1: 954493
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 27
Sequence: agccaggcgagatatgatctatatcaatttctcatctataatgctttgttagtatctcgtCgccgacttaataaagagaga
                             -35                  -10       +1                   
Evidence: [HIPP]
[ICWHO]
[IHBCE]
[TIM]
Reference(s): [4] Huerta AM., et al., 2003
[5] Kaiser M., et al., 1995
[6] Kaiser M., et al., 1997
[1] Sawers G., et al., 1989
[7] Sawers G., et al., 1992
Terminator(s)
Type: rho-independent
Sequence: tcgcgctaaaAAAGGCCCCACTTTCGTGGAGCCTTTATTGTACGCTTTTTACTGTACGATTTCAGTCAAAtctaattaca
Note(s): This terminator presents a double stem-loop structure.
Reference(s): [1] Sawers G., et al., 1989
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 ArcA-phosphorylated activator focAp1 954492 954506 -6.0 ataatgctttGTTAGTATCTCGTCGccgacttaat nd [GEA], [APIORCISFBSCS] [8]
remote ArcA-phosphorylated activator focAp1 954600 954614 -114.0 tttatttttaTTTGGATAATCAAATatttactccg nd [EME], [GEA], [AIBSPD], [APIORCISFBSCS], [BPP], [CCE] [7], [8], [9], [10], [11], [12]
remote ArcA-phosphorylated activator focAp1 954737 954751 -251.0 tataaggttaAATATCGGTAATTTGtatttaataa nd [EME], [GEA], [AIBSPD], [APIORCISFBSCS], [CCE] [8], [9]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cyclic-AMP activator focAp1 954523 954544 -40.5 aagccaggcgAGATATGATCTATATCAATTTCtcatctataa nd [GEA], [AIBSCS], [APIORCISFBSCS], [BCE], [SM] [13], [14]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR activator focAp1 954527 954540 -40.5 caggcgagatATGATCTATATCAAtttctcatct nd [GEA], [APIORCISFBSCS], [BCE], [SM] [8]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote IHF activator focAp1 954599 954611 -112.5 atttttatttGGATAATCAAATAtttactccgt nd [GEA], [APIORCISFBSCS], [BCE], [BPP], [SM] nd
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NarL-phosphorylated repressor focAp1 954510 954516 -20.0 tttctcatctATAATGCtttgttagta nd [GEA], [APIORCISFBSCS], [BPP] [5]
proximal NarL-phosphorylated repressor focAp1 954527 954533 -37.0 gatatgatctATATCAAtttctcatct nd [GEA], [APIORCISFBSCS], [BPP] [5]
remote NarL-phosphorylated repressor focAp1 954591 954597 -101.0 aatcaaatatTTACTCCgtatttgcat nd [GEA], [APIORCISFBSCS], [BPP] [5]
remote NarL-phosphorylated repressor focAp1 954642 954648 -152.0 ggaaaaaattCAACTCAtttgttaatt nd [GEA], [APIORCISFBSCS], [BPP] [5]
remote NarL-phosphorylated repressor focAp1 954716 954722 -226.0 taataaatacGATCGATattgttactt nd [GEA], [APIORCISFBSCS], [BPP] [5]
remote NarL-phosphorylated repressor focAp1 954725 954731 -235.0 atttgtatttAATAAATacgatcgata nd [GEA], [APIORCISFBSCS], [BPP] [5]
remote NarL-phosphorylated repressor focAp1 954743 954749 -253.0 taaggttaaaTATCGGTaatttgtatt nd [GEA], [APIORCISFBSCS], [BPP] [5]
remote NarL-phosphorylated repressor focAp1 954760 954766 -270.0 taaaataattGTAATTAtaaggttaaa nd [GEA], [APIORCISFBSCS], [BPP] [5]
remote NarL-phosphorylated repressor focAp1 954776 954782 -286.0 catatatttgCATTAATaaaataattg nd [GEA], [APIORCISFBSCS], [BPP] [5]
remote NarL-phosphorylated repressor focAp1 954836 954842 -346.0 tgtaggcttaATGATTAgtctgagtta nd [GEA], [APIORCISFBSCS], [BPP] [5]
remote NarL-phosphorylated repressor focAp1 954838 954844 -348.0 aatgtaggctTAATGATtagtctgagt nd [GEA], [APIORCISFBSCS], [BPP] [5]


Transcription unit          
Name: focA-pflB
Synonym(s): pfl
Gene(s): pflB, focA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The focA gene and pflB gene are cotranscribed, but pflB is also transcribed alone.
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for focA . This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Sawers G., et al., 1989
Promoter
Name: focAp2
+1: 954503
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 37
Sequence: cgggcctataagccaggcgagatatgatctatatcaatttctcatctataatgctttgttAgtatctcgtcgccgacttaa
                        -35                    -10          +1                   
Note(s): Transcription initiation from this promoter is weak and constitutive Kaiser M,1995.
Evidence: [HIPP]
[ICWHO]
[IHBCE]
[RS-EPT-CBR]
[TIM]
Reference(s): [4] Huerta AM., et al., 2003
[15] Kaiser M., et al., 1995
[2] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: tcgcgctaaaAAAGGCCCCACTTTCGTGGAGCCTTTATTGTACGCTTTTTACTGTACGATTTCAGTCAAAtctaattaca
Note(s): This terminator presents a double stem-loop structure.
Reference(s): [1] Sawers G., et al., 1989
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 ArcA-phosphorylated activator focAp2 954492 954506 5.0 ataatgctttGTTAGTATCTCGTCGccgacttaat nd [GEA], [APIORCISFBSCS] [8]


Transcription unit          
Name: focA-pflB
Synonym(s): pfl
Gene(s): pflB, focA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The focA gene and pflB gene are cotranscribed, but pflB is also transcribed alone.
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for focA . This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Sawers G., et al., 1989
Promoter
Name: focAp3
+1: 954814
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 348
Sequence: taaaatcaaatagcctacgcaatgtaggcttaatgattagtctgagttatattacggggcGtttttttaatgccccgcttt
                      -35                       -10         +1                   
Evidence: [HIPP]
[ICWHO]
[IHBCE]
[TIM]
Reference(s): [4] Huerta AM., et al., 2003
[5] Kaiser M., et al., 1995
[1] Sawers G., et al., 1989
[7] Sawers G., et al., 1992
Terminator(s)
Type: rho-independent
Sequence: tcgcgctaaaAAAGGCCCCACTTTCGTGGAGCCTTTATTGTACGCTTTTTACTGTACGATTTCAGTCAAAtctaattaca
Note(s): This terminator presents a double stem-loop structure.
Reference(s): [1] Sawers G., et al., 1989
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 FNR activator focAp3 954866 954879 -58.5 gcattctgggCAAAATAAAATCAAatagcctacg nd [GEA], [BCE], [SM] [8]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote NarL-phosphorylated repressor focAp3 954510 954516 302.0 tttctcatctATAATGCtttgttagta nd [GEA], [APIORCISFBSCS], [BPP] [5]
remote NarL-phosphorylated repressor focAp3 954527 954533 285.0 gatatgatctATATCAAtttctcatct nd [GEA], [APIORCISFBSCS], [BPP] [5]
remote NarL-phosphorylated repressor focAp3 954591 954597 221.0 aatcaaatatTTACTCCgtatttgcat nd [GEA], [APIORCISFBSCS], [BPP] [5]
remote NarL-phosphorylated repressor focAp3 954642 954648 170.0 ggaaaaaattCAACTCAtttgttaatt nd [GEA], [APIORCISFBSCS], [BPP] [5]
remote NarL-phosphorylated repressor focAp3 954716 954722 96.0 taataaatacGATCGATattgttactt nd [GEA], [APIORCISFBSCS], [BPP] [5]
remote NarL-phosphorylated repressor focAp3 954725 954731 87.0 atttgtatttAATAAATacgatcgata nd [GEA], [APIORCISFBSCS], [BPP] [5]
remote NarL-phosphorylated repressor focAp3 954743 954749 69.0 taaggttaaaTATCGGTaatttgtatt nd [GEA], [APIORCISFBSCS], [BPP] [5]
remote NarL-phosphorylated repressor focAp3 954760 954766 52.0 taaaataattGTAATTAtaaggttaaa nd [GEA], [APIORCISFBSCS], [BPP] [5]
remote NarL-phosphorylated repressor focAp3 954776 954782 36.0 catatatttgCATTAATaaaataattg nd [GEA], [APIORCISFBSCS], [BPP] [5]
proximal NarL-phosphorylated repressor focAp3 954836 954842 -25.0 tgtaggcttaATGATTAgtctgagtta nd [GEA], [APIORCISFBSCS], [BPP] [5]
proximal NarL-phosphorylated repressor focAp3 954838 954844 -27.0 aatgtaggctTAATGATtagtctgagt nd [GEA], [APIORCISFBSCS], [BPP] [5]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
Evidence: [ICA] Inferred by computational analysis
Reference(s): [16] Merino E, et al., 2005
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -11.8 953738 953782 cttcgcatccCCGGAATTTTGGACCGCAGTCGGTTCTGCACCGGAAAATTTTTCtcacctgacc
  anti-terminator -9.1 953763 953806 cccgatgggtATTGTAATCCGCGACTTCGCATCCCCGGAATTTTGGACCGCAGtcggttctgc
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"




Reference(s)    

 [1] Sawers G., Bock A., 1989, Novel transcriptional control of the pyruvate formate-lyase gene: upstream regulatory sequences and multiple promoters regulate anaerobic expression., J Bacteriol 171(5):2485-98

 [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] Bradley MD., Beach MB., de Koning AP., Pratt TS., Osuna R., 2007, Effects of Fis on Escherichia coli gene expression during different growth stages., Microbiology 153(Pt 9):2922-40

 [4] 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

 [5] Kaiser M., Sawers G., 1995, Nitrate repression of the Escherichia coli pfl operon is mediated by the dual sensors NarQ and NarX and the dual regulators NarL and NarP., J Bacteriol 177(13):3647-55

 [6] Kaiser M., Sawers G., 1997, Overlapping promoters modulate Fnr- and ArcA-dependent anaerobic transcriptional activation of the focApfl operon in Escherichia coli., Microbiology 143 ( Pt 3):775-83

 [7] Sawers G., Suppmann B., 1992, Anaerobic induction of pyruvate formate-lyase gene expression is mediated by the ArcA and FNR proteins., J Bacteriol 174(11):3474-8

 [8] Drapal N., Sawers G., 1995, Promoter 7 of the Escherichia coli pfl operon is a major determinant in the anaerobic regulation of expression by ArcA., J Bacteriol 177(18):5338-41

 [9] Federowicz S., Kim D., Ebrahim A., Lerman J., Nagarajan H., Cho BK., Zengler K., Palsson B., 2014, Determining the control circuitry of redox metabolism at the genome-scale., PLoS Genet 10(4):e1004264

 [10] Drapal N., Sawers G., 1995, Purification of ArcA and analysis of its specific interaction with the pfl promoter-regulatory region., Mol Microbiol 16(3):597-607

 [11] Sawers G., 1993, Specific transcriptional requirements for positive regulation of the anaerobically inducible pfl operon by ArcA and FNR., Mol Microbiol 10(4):737-47

 [12] Sirko A., Zehelein E., Freundlich M., Sawers G., 1993, Integration host factor is required for anaerobic pyruvate induction of pfl operon expression in Escherichia coli., J Bacteriol 175(18):5769-77

 [13] Sawers G., Kaiser M., Sirko A., Freundlich M., 1997, Transcriptional activation by FNR and CRP: reciprocity of binding-site recognition., Mol Microbiol 23(4):835-45

 [14] Zheng D., Constantinidou C., Hobman JL., Minchin SD., 2004, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling., Nucleic Acids Res 32(19):5874-93

 [15] Kaiser M., Sawers G., 1995, Fnr activates transcription from the P6 promoter of the pfl operon in vitro., Mol Microbiol 18(2):331-42

 [16] Merino E, Yanofsky C., 2005, Transcription attenuation: a highly conserved regulatory strategy used by bacteria., Trends Genet. 2005 May;21(5):260-4.


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