RegulonDB RegulonDB 11.2: 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 Jones SA, Gibson T, Maltby RC, Chowdhury FZ, Stewart V, Cohen PS, Conway T,2011
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.
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for narG . 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.
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: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [4] Huerta AM., et al., 2003
[5] Rabin RS., et al., 1992
[6] Walker MS., et al., 1991
Terminator(s)
Type: rho-independent
Sequence: gctcgtcactAAGCGAATTTTAGTTCACATAGACCCTGCTTCGGCGGGGTTTTTTTATGGGCACGgtgcggggtg
Reference(s): [7] Feng CQ., et al., 2019
[8] Lesnik EA., et al., 2001
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 narGp 1279759 1279772 -41.5 cccatcactcTTGATCGTTATCAAttcccacgct nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [16], [17]
[Fis,-] 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 Fis repressor narGp 1279697 1279711 -103.0 gttatgtggtGGCTGTTAATTATCCtaaaggggta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [13]
proximal Fis repressor narGp 1279734 1279748 -66.0 ttaggaatttACTTTATTTTTCATCcccatcactc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [13]
[IHF,+] 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 IHF activator narGp 1279676 1279688 -125.0 aaacgtcttaATTTACAGTCTGTtatgtggtgg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [5], [11], [12]
[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
remote NarL-phosphorylated activator narGp 1279596 1279602 -208.0 attaatatgtTACCCATggggaatact nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3], [5], [10]
remote NarL-phosphorylated activator narGp 1279609 1279615 -195.0 ccatggggaaTACTCCTtaatacccat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [2], [3], [5], [10]
remote NarL-phosphorylated activator narGp 1279619 1279625 -185.0 tactccttaaTACCCATctgcataaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [2], [3], [5], [10]
remote NarL-phosphorylated activator narGp 1279703 1279709 -101.0 tggtggctgtTAATTATcctaaagggg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [2], [3], [5], [10], [14], [15]
proximal NarL-phosphorylated activator narGp 1279715 1279721 -89.0 attatcctaaAGGGGTAtcttaggaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [2], [3], [5], [10]
proximal NarL-phosphorylated activator narGp 1279725 1279731 -79.0 aggggtatctTAGGAATttactttatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3], [5], [10]
proximal NarL-phosphorylated activator narGp 1279733 1279739 -71.0 cttaggaattTACTTTAtttttcatcc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3], [5], [10]
proximal NarL-phosphorylated activator narGp 1279747 1279753 -57.0 ttatttttcaTCCCCATcactcttgat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3], [5], [10]
[RstA,+] 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 RstA-phosphorylated activator narGp 1279523 1279539 -276.0 ctttttttatGCGTCATTTAGTTACAAcatactaatg nd [COMP-HINF-SIMILAR-TO-CONSENSUS] nd [9]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

 [EXP-IMP-SITE-MUTATION] Site mutation

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] 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] 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] 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

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

 [7] 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

 [8] 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

 [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] 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

 [17] 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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