RegulonDB RegulonDB 11.2: Operon Form
   

napFDAGHBC-ccmABCDEFGH operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: napFDAGHBC-ccmABCDEFGH
Synonym(s): aeg-46.5
Gene(s): ccmH, ccmG, ccmF, ccmE, ccmD, ccmC, ccmB, ccmA, napC, napB, napH, napG, napA, napD, napF   Genome Browser M3D Gene expression COLOMBOS
Note(s): Based on ChIP-chip and consensus sequences (Virtual Footprint), a site of NsrR upstream of the napF gene was identified Partridge JD,2009 However, this gene exerts its control from three promoters, and it is not known which of them is negatively controlled by NsrR.
Reference(s): [1] Darwin AJ., et al., 1995
[2] Grove J., et al., 1996
Promoter
Name: napFp1
+1: 2303574
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 77
Sequence: acaggttttaccccgatcggggtatgcatctttgacacatcctttaatatcttagcggctAtaaaaatggcttattaatta
                             -35                     -10    +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Choe M., et al., 1993
[1] Darwin AJ., et al., 1995
[4] Darwin AJ., et al., 1998
[5] Huerta AM., et al., 2003
[6] Stewart V., et al., 2003
TF binding sites (TFBSs)
[FNR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR activator napFp1 2303632 2303645 -64.5 cgccactcttTTGATCCTGCTACAggttttaccc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IMP-SITE-MUTATION] C [4], [6]
[FlhDC,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FlhDC activator napFp1 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [8]
[ModE,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote ModE-molybdate activator napFp1 2303696 2303719 -133.5 gtgaatcaatCGCTATATAAATATATTTATAACCatttgaaatg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [7]
[NarL,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NarL-phosphorylated repressor napFp1 2303611 2303617 -40.0 ttaccccgatCGGGGTAtgcatctttg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] W [1], [4], [6]
proximal NarL-phosphorylated repressor napFp1 2303620 2303626 -49.0 ctacaggtttTACCCCGatcggggtat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] W [1], [4], [6]
[NarP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NarP-phosphorylated activator napFp1 2303606 2303621 -40.0 ggttttacccCGATCGGGGTATGCATctttgacaca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] W [4], [6]
proximal NarP-phosphorylated activator napFp1 2303615 2303630 -49.0 cctgctacagGTTTTACCCCGATCGGggtatgcatc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] W [4], [6]


Transcription unit          
Name: napFDAGHBC-ccmABCDEFGH
Gene(s): ccmH, ccmG, ccmF, ccmE, ccmD, ccmC, ccmB, ccmA, napC, napB, napH, napG, napA, napD, napF   Genome Browser M3D Gene expression COLOMBOS
Note(s): Based on ChIP-chip and consensus sequences (Virtual Footprint), a site of NsrR upstream of the napF gene was identified Partridge JD,2009 However, this gene exerts its control from three promoters, and it is not known which of them is negatively controlled by NsrR.
Reference(s): [1] Darwin AJ., et al., 1995
[2] Grove J., et al., 1996
Promoter
Name: napFp2
+1: 2303577
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 80
Sequence: gctacaggttttaccccgatcggggtatgcatctttgacacatcctttaatatcttagcgGctataaaaatggcttattaa
                                -35                     -10 +1                   
Note(s): Nitrate causes repression of the napFp2 promoter in a NarL- or a NarP-protein-dependent way, whereas repression of the same promoter by nitrite is only dependent on the NarP protein Stewart V,2003
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [4] Darwin AJ., et al., 1998
[5] Huerta AM., et al., 2003
[6] Stewart V., et al., 2003
TF binding sites (TFBSs)
[FlhDC,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FlhDC activator napFp2 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [8]
[ModE,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote ModE-molybdate activator napFp2 2303696 2303719 -130.5 gtgaatcaatCGCTATATAAATATATTTATAACCatttgaaatg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6]
[NarL,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NarL-phosphorylated repressor napFp2 2303611 2303617 -37.0 ttaccccgatCGGGGTAtgcatctttg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] W [6]
proximal NarL-phosphorylated repressor napFp2 2303620 2303626 -46.0 ctacaggtttTACCCCGatcggggtat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] W [6]
[NarP,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NarP-phosphorylated repressor napFp2 2303606 2303621 -37.0 ggttttacccCGATCGGGGTATGCATctttgacaca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] W [6]
proximal NarP-phosphorylated repressor napFp2 2303615 2303630 -46.0 cctgctacagGTTTTACCCCGATCGGggtatgcatc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] W [6]


Transcription unit          
Name: napFDAGHBC
Gene(s): napC, napB, napH, napG, napA, napD, napF   Genome Browser M3D Gene expression COLOMBOS
Note(s): Based on ChIP-chip and consensus sequences (Virtual Footprint), a site of NsrR upstream of the napF gene was identified Partridge JD,2009 However, this gene exerts its control from three promoters, and it is not known which of them is negatively controlled by NsrR.
Promoter
Name: napFp3
+1: 2303695
Distance from start of the gene: 198
Sequence: agagcaaaccagcagaaatatctctggtgaatcaatcgctatataaatatatttataaccAtttgaaatgtgagcaaaagc
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [9] Giel JL., et al., 2006
TF binding sites (TFBSs)
[IscR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IscR repressor napFp3 2303677 2303701 7.0 aaatatatttATAACCATTTGAAATGTGAGCAAAAgcccgttttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [9]


Transcription unit       
Name: ccmABCDEFGH
Gene(s): ccmH, ccmG, ccmF, ccmE, ccmD, ccmC, ccmB, ccmA   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: ccmAp
+1: Unknown
Sigma Factor: Sigma70 Sigmulon
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [10] Tanapongpipat S., et al., 1998


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [EXP-IDA] Inferred from direct assay

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-CHIP-SEQ] high throughput ChIP-seq evidence

 [EXP-IMP-SITE-MUTATION] Site mutation

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

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


Reference(s)    

 [1] Darwin AJ., Stewart V., 1995, Nitrate and nitrite regulation of the Fnr-dependent aeg-46.5 promoter of Escherichia coli K-12 is mediated by competition between homologous response regulators (NarL and NarP) for a common DNA-binding site., J Mol Biol 251(1):15-29

 [2] Grove J., Tanapongpipat S., Thomas G., Griffiths L., Crooke H., Cole J., 1996, Escherichia coli K-12 genes essential for the synthesis of c-type cytochromes and a third nitrate reductase located in the periplasm., Mol Microbiol 19(3):467-81

 [3] Choe M., Reznikoff WS., 1993, Identification of the regulatory sequence of anaerobically expressed locus aeg-46.5., J Bacteriol 175(4):1165-72

 [4] Darwin AJ., Ziegelhoffer EC., Kiley PJ., Stewart V., 1998, Fnr, NarP, and NarL regulation of Escherichia coli K-12 napF (periplasmic nitrate reductase) operon transcription in vitro., J Bacteriol 180(16):4192-8

 [5] 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

 [6] Stewart V., Bledsoe PJ., Williams SB., 2003, Dual overlapping promoters control napF (periplasmic nitrate reductase) operon expression in Escherichia coli K-12., J Bacteriol 185(19):5862-70

 [7] McNicholas PM., Gunsalus RP., 2002, The molybdate-responsive Escherichia coli ModE transcriptional regulator coordinates periplasmic nitrate reductase (napFDAGHBC) operon expression with nitrate and molybdate availability., J Bacteriol 184(12):3253-9

 [8] Pruss BM., Liu X., Hendrickson W., Matsumura P., 2001, FlhD/FlhC-regulated promoters analyzed by gene array and lacZ gene fusions., FEMS Microbiol Lett 197(1):91-7

 [9] Giel JL., Rodionov D., Liu M., Blattner FR., Kiley PJ., 2006, IscR-dependent gene expression links iron-sulphur cluster assembly to the control of O-regulated genes in Escherichia coli., Mol Microbiol 60(4):1058-75

 [10] Tanapongpipat S., Reid E., Cole JA., Crooke H., 1998, Transcriptional control and essential roles of the Escherichia coli ccm gene products in formate-dependent nitrite reduction and cytochrome c synthesis., Biochem J 334 ( Pt 2):355-65

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