RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: narGHJI
Synonym(s): OP00060, chlC, narG, narGHIJ
Gene(s): narG, narH, narJ, narI   Genome Browser M3D Gene expression COLOMBOS
Note(s): IHF alters the DNA topology of the narGHJI promoter upstream region and at the same time acts as a transcriptional enhancer of NarL and FNR from the narG promoter upon nitrate availability and under anaerobic conditions, respectively Schroder I,1993
The NarX-NarL complex is necessary for colonization and competitive fitness in the streptomycin-treated mouse intestine through narG activation 21825069
A narG mutant responded poorly to nitrite, consistent with nitrite reduction by NarGHI being the major source of NO in the cytoplasm Vine CE,2011.
Reference(s): [1] Bonnefoy V., et al., 1997
[2] Darwin AJ., et al., 1996
[3] Li J., et al., 1994
Promoter
Name: narGp
+1: 1279807
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 57
Sequence: tccccatcactcttgatcgttatcaattcccacgctgtttcagagcgttaccttgcccttAaacattagcaatgtcgattt
                           -35                   -10        +1                   
Evidence: [HIPP]
[TIM]
Reference(s): [4] Rabin RS., et al., 1992
[5] Walker MS., et al., 1991
Terminator(s)
Type: rho-independent
Sequence: gctcgtcactAAGCGAATTTTAGTTCACATAGACCCTGCTTCGGCGGGGTTTTTTTATGGGCACGgtgcggggtg
Reference(s): [6] Feng CQ., et al., 2019
[7] Lesnik EA., et al., 2001
TF binding sites (TFBSs)
[FNR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR activator narGp 1279759 1279772 -41.5 cccatcactcTTGATCGTTATCAAttcccacgct nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [16], [17], [18], [19]
[Fis,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Fis repressor narGp 1279697 1279711 -103.0 gttatgtggtGGCTGTTAATTATCCtaaaggggta nd [AIBSCS], [CV(GEA)], [GEA] [13]
proximal Fis repressor narGp 1279734 1279748 -66.0 ttaggaatttACTTTATTTTTCATCcccatcactc nd [AIBSCS], [CV(GEA)], [GEA] [13]
[IHF,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote IHF activator narGp 1279676 1279688 -125.0 aaacgtcttaATTTACAGTCTGTtatgtggtgg nd [APIORCISFBSCS], [BCE], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [4], [11], [12]
[NarL,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote NarL-Phosphorylated activator narGp 1279591 1279606 -208.0 gagccattaaTATGTTACCCATGGGGaatactcctt nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [3], [4], [10]
remote NarL-Phosphorylated activator narGp 1279604 1279619 -195.0 gttacccatgGGGAATACTCCTTAATacccatctgc nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [2], [3], [4], [10]
remote NarL-Phosphorylated activator narGp 1279614 1279629 -185.0 gggaatactcCTTAATACCCATCTGCataaaaatct nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [2], [3], [4], [10]
remote NarL-Phosphorylated activator narGp 1279698 1279713 -101.0 ttatgtggtgGCTGTTAATTATCCTAaaggggtatc nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [2], [3], [4], [10], [14], [15]
proximal NarL-Phosphorylated activator narGp 1279710 1279725 -89.0 tgttaattatCCTAAAGGGGTATCTTaggaatttac nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [2], [3], [4], [10]
proximal NarL-Phosphorylated activator narGp 1279720 1279735 -79.0 cctaaaggggTATCTTAGGAATTTACtttatttttc nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [3], [4], [10]
proximal NarL-Phosphorylated activator narGp 1279728 1279743 -71.0 ggtatcttagGAATTTACTTTATTTTtcatccccat nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [3], [4], [10]
proximal NarL-Phosphorylated activator narGp 1279742 1279757 -57.0 ttactttattTTTCATCCCCATCACTcttgatcgtt nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [3], [4], [10]
[RstA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote RstA-Phosphorylated activator narGp 1279523 1279539 -276.0 ctttttttatGCGTCATTTAGTTACAAcatactaatg nd [APIORCISFBSCS] [8], [9]


Evidence    

 [HIPP] Human inference of promoter position

 [TIM] Transcription initiation mapping

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [BPP] Binding of purified proteins

 [CV(GEA)] cross validation(GEA)

 [CV(GEA/SM)] cross validation(GEA/SM)

 [CV(SM)] cross validation(SM)

 [GEA] Gene expression analysis

 [SM] Site mutation

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BCE] Binding of cellular extracts


Reference(s)    

 [1] Bonnefoy V., Ratouchniak J., Blasco F., Chippaux M., 1997, Organization of the nar genes at the chlZ locus., FEMS Microbiol Lett 147(1):147-9

 [2] Darwin AJ., Li J., Stewart V., 1996, Analysis of nitrate regulatory protein NarL-binding sites in the fdnG and narG operon control regions of Escherichia coli K-12., Mol Microbiol 20(3):621-32

 [3] Li J., Kustu S., Stewart V., 1994, In vitro interaction of nitrate-responsive regulatory protein NarL with DNA target sequences in the fdnG, narG, narK and frdA operon control regions of Escherichia coli K-12., J Mol Biol 241(2):150-65

 [4] Rabin RS., Collins LA., Stewart V., 1992, In vivo requirement of integration host factor for nar (nitrate reductase) operon expression in Escherichia coli K-12., Proc Natl Acad Sci U S A 89(18):8701-5

 [5] Walker MS., DeMoss JA., 1991, Promoter sequence requirements for Fnr-dependent activation of transcription of the narGHJI operon., Mol Microbiol 5(2):353-60

 [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] Ogasawara H., Hasegawa A., Kanda E., Miki T., Yamamoto K., Ishihama A., 2007, Genomic SELEX search for target promoters under the control of the PhoQP-RstBA signal relay cascade., J Bacteriol 189(13):4791-9

 [9] Oshima T., Aiba H., Masuda Y., Kanaya S., Sugiura M., Wanner BL., Mori H., Mizuno T., 2002, Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12., Mol Microbiol 46(1):281-91

 [10] Stewart V., 1982, Requirement of Fnr and NarL functions for nitrate reductase expression in Escherichia coli K-12., J Bacteriol 151(3):1320-5

 [11] Schroder I., Darie S., Gunsalus RP., 1993, Activation of the Escherichia coli nitrate reductase (narGHJI) operon by NarL and Fnr requires integration host factor., J Biol Chem 268(2):771-4

 [12] Zhang X., DeMoss JA., 1996, Structure modification induced in the narG promoter by binding of integration host factor and NARL-P., J Bacteriol 178(13):3971-3

 [13] 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

 [14] Darwin AJ., Tyson KL., Busby SJ., Stewart V., 1997, Differential regulation by the homologous response regulators NarL and NarP of Escherichia coli K-12 depends on DNA binding site arrangement., Mol Microbiol 25(3):583-95

 [15] Rabin RS., Stewart V., 1993, Dual response regulators (NarL and NarP) interact with dual sensors (NarX and NarQ) to control nitrate- and nitrite-regulated gene expression in Escherichia coli K-12., J Bacteriol 175(11):3259-68

 [16] Eiglmeier K., Honore N., Iuchi S., Lin EC., Cole ST., 1989, Molecular genetic analysis of FNR-dependent promoters., Mol Microbiol 3(7):869-78

 [17] Lamberg KE., Kiley PJ., 2000, FNR-dependent activation of the class II dmsA and narG promoters of Escherichia coli requires FNR-activating regions 1 and 3., Mol Microbiol 38(4):817-27

 [18] Li SF., DeMoss JA., 1988, Location of sequences in the nar promoter of Escherichia coli required for regulation by Fnr and NarL., J Biol Chem 263(27):13700-5

 [19] Melville SB., Gunsalus RP., 1996, Isolation of an oxygen-sensitive FNR protein of Escherichia coli: interaction at activator and repressor sites of FNR-controlled genes., Proc Natl Acad Sci U S A 93(3):1226-31

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