RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: nrfABCDEFG
Synonym(s): OP00279, nrf
Gene(s): nrfA, nrfB, nrfC, nrfD, nrfE, nrfF, nrfG   Genome Browser M3D Gene expression COLOMBOS
Note(s): nrfA operon regulation is complex and is affected by different protein factors. Under anaerobic conditions, FNR activates binding at the -41.5 site, but its activation is repressed by IHF at the -55 site. When nitrate or nitrite is present, NarL is activated (via NarX or NarQ) and, upon binding to its target site, IHF is displaced and derepresses the FNR site to allow its dependent activation. Fis binding plays a central role in the catabolite repression of the nrf operon. Therefore, activation involving FNR, NarL, and IHF is thwarted by Fis when it binds to its target at position -15 and blocks access to the nrf promoter -10 element Browning DF,2005.
IHF can also activate the transcription of the nrf operon in an FNR-dependent way when it is bound to the site located at bp -179 from the promoter, but only when NarL and NarP are absent Browning DF,2006
nrfA expression is downregulated by NsrR, which is independent of IHF-dependent regulation Browning DF,2010. NsrR acts as a fine-tuner because it modulates nrfA activity rather than switching it off completely Browning DF,2010.
Based on a DNA sampling method, HU and YfhH were determined to be regulating the nrfA gene in vivo Browning DF,2010. HU activates nrfABCDEFG operon expression during exponential growth 19194530.
nrfABCDEFG was significantly upregulated in response to quinonas anthraquinone-2-sulfonate (AQSim) reduction and azo dye acid red 18 (AR 18) decolorization under anaerobic conditions 23820558.
Reference(s): [1] Hussain H., et al., 1994
Promoter
Name: nrfAp
+1: 4287671
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 93
Sequence: atgcacttacaattgattaaagacaacattcacagtgtggttatttgttacacataggggCgagcaatgtcatgacagtgt
                            -35                  -10        +1                   
Note(s): Nitrate causes repression of the nrfAp promoter in a NarL- or a NarP-protein-dependent way, while repression of the same promoter by nitrite is mainly dependent on the NarP protein Stewart V,2003
Evidence: [IMP]
[TIM]
Reference(s): [2] Darwin A., et al., 1993
[3] Tyson KL., et al., 1994
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 FNR1 activator nrfAp 4287623 4287636 -41.5 gcacttacaaTTGATTAAAGACAAcattcacagt nd [BCE], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [10], [11]
[Fis,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fis1 repressor nrfAp 4287649 4287663 -15.0 ttcacagtgtGGTTATTTGTTACACataggggcga nd [BPP], [GEA] [4], [9], [10]
[FlhDC,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FlhDC1 activator nrfAp nd nd nd nd nd [GEA] [15]
[IHF,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote IHF1 activator nrfAp 4287538 4287550 -127.0 tgattaattcTTTGAGGAACATGcagttatgca nd [AIBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [SM] [4], [5], [6]
[IHF,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IHF1 repressor nrfAp 4287610 4287622 -55.0 tggtattttaCATGCACTTACAAttgattaaag nd [BPP], [GEA] [4], [9], [10]
[NarL,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NarL-Phosphorylated activator nrfAp 4287584 4287599 -79.0 gaggaagataCTGACTAACTCTAAAGtggtatttta nd [AIBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [SM] [3], [9], [10], [11], [12], [13]
proximal NarL-Phosphorylated2 activator nrfAp 4287593 4287608 -70.0 actgactaacTCTAAAGTGGTATTTTacatgcactt nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [SM] [3], [9], [10], [11], [12], [13]
proximal NarL-Phosphorylated3 activator nrfAp 4287613 4287628 -50.0 tattttacatGCACTTACAATTGATTaaagacaaca nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [SM] [3], [9], [11], [12], [13]
[NarL,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NarL-Phosphorylated1 repressor nrfAp 4287613 4287628 -50.0 tattttacatGCACTTACAATTGATTaaagacaaca nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [SM] [3], [9], [11], [12], [13]
proximal NarL-Phosphorylated2 repressor nrfAp 4287641 4287656 -22.0 agacaacattCACAGTGTGGTTATTTgttacacata nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [SM] [3], [9], [11], [12], [13]
[NarP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NarP-Phosphorylated activator nrfAp 4287584 4287599 -79.0 gaggaagataCTGACTAACTCTAAAGtggtatttta nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [SM] [3], [9], [10], [11], [12], [13]
proximal NarP-Phosphorylated2 activator nrfAp 4287593 4287608 -70.0 actgactaacTCTAAAGTGGTATTTTacatgcactt nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [SM] [3], [9], [10], [11], [12], [13]
[NsrR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote NsrR repressor nrfAp 4287545 4287556 -121.0 ttctttgaggAACATGCAGTTAtgcatgctgt nd [APIORCISFBSCS], [CV(GEA/ROMA)], [GEA] [7], [8]
proximal NsrR repressor nrfAp 4287599 4287617 -63.0 taactctaaaGTGGTATTTTACATGCACTtacaattgat nd [APIORCISFBSCS], [BCE], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [SM] [8], [14]
Note(s): 1nrf regulation is totally dependent on FNR at this site (-41.5) under anaerobic conditions. FNR and NarL/NarP act by promoting the open complex formation by RNA polymerase at the nrf promoter. Although it seems that NarL and FNR can bind to their targets independently, NarL is unable to activate the nrf promoter in the absence of FNR Browning DF,2005. Based on DNase I footprinting Browning DF,2005 suggest that IHF alters the binding of FNR without displacing it from its site. In adittion, NarL binding prevents IHF binding but has little or no effect on FNR or Fis binding.1Fis binding to this site weakly represses the nrfAp promoter and strongly represses acsP1, a promoter that overlaps and is divergent to nrfAp.
Either IHF or Fis can repress FNR-dependent open complex formation. NarL binding to its target reverses IHF-dependent repression but does not relieve Fis-dependent repression Browning DF,2005.1The regulatory effect of FlhDC in nrfA operon transcription has been proved only by microarray analysis by Pruss BM,2001.1IHF, located at -127 from the nrfAp promoter, is necessary to activate the FNR-dependent transcription of the nrfABCDEFG operon , but only in the absence of NarL/NarP Browning DF,20061IHF binding to a site located -55 bp from the promoter weakly represses the nrfAp promoter and strongly represses acsP1, a promoter that overlaps and is divergent to nrfAp.
NarL and IHF cannot bind together, contrary to other protein regulators that can bind together to form ternary complexes. Fis binds independently to FNR and IHF. Browning DF,2005 supposes that Fis blocks access of RNAP to the nrf promoter. Based on DNase footprinting Browning DF,2005 it is suggested that IHF alters the binding of FNR without displacing it from its site. In addition, NarL binding prevents IHF binding but has little or no effect on FNR or Fis binding. Either Fis or IHF at -55 can repress FNR-dependent open complex formation. NarL binding to its target reverses IHF-dependent repression but does not relieve Fis-dependent repression Browning DF,2005
2The maximum nrfA expression is achieved at low nitrate concentrations through NarP and mainly through NarL. Wang and Gunsalus Wang H,2000 reported that the nitrite is a less effective inductor of nrfA expression, although in a earlier report Page et al. 2173895 reported that this molecule was the primary signal. The sites at -70 and -79 are recognized by NarL and NarP, but NarL has the highest affinity for them.

nrf expression is increased in response to nitrite or nitrate ions by NarL or NarP. FNR and NarL/NarP act by promoting open complex formation by RNAP at the nrf promoter. Although it seems that NarL and FNR can bind to their targets independently, NarL is unable to activate the nrf promoter in the absence of FNR Browning DF,2005. NarL and IHF cannot bind together; the other protein regulators can bind together to form ternary complexes. Fis binds independently of FNR and IHF. Browning DF,2005 supposed that Fis blocks access of RNAP to the nrf promoter.
3At low levels of nitrate, NarL activates nrfA expression and at high levels of nitrate NarL represses it.1At low levels of nitrate, NarL activates nrfA expression and at high levels of nitrate NarL represses it.
2The -22 and -50 NarL sites are needed for optimal repression of nrfA expression. At high nitrate concentrations NarL can repress nrfA expression, but NarP cannot Wang H,20002NarP appears to weakly antagonize the activation of nrfA by NarL at low nitrate concentrations Wang H,2000
nrf expression is increased in response to nitrite or nitrate ions by NarL or NarP. FNR and NarL/NarP act by promoting open complex formation by RNAP at the nrf promoter. Although it seems that NarL and FNR can bind to their targets independently, NarL is unable to activate the nrf promoter in the absence of FNR Browning DF,2005. NarL and IHF cannot bind together, and the other protein regulator can bind together to form ternary complexes. Fis binds independently of FNR and IHF. Browning DF,2005 supposed that Fis block access of RNAP to the nrf promoter.
1IHF, located at -127 from the nrfAp promoter, is necessary to activate the FNR-dependent transcription of the nrfABCDEFG operon , but only in the absence of NarL/NarP Browning DF,2006
5NarP appears to weakly antagonize the activation of nrfA by NarL at low nitrate concentrations Wang H,2000
nrf expression is increased in response to nitrite or nitrate ions by NarL or NarP. FNR and NarL/NarP act by promoting open complex formation by RNAP at the nrf promoter. Although it seems that NarL and FNR can bind to their targets independently, NarL is unable to activate the nrf promoter in the absence of FNR Browning DF,2005. NarL and IHF cannot bind together, and the other protein regulator can bind together to form ternary complexes. Fis binds independently of FNR and IHF. Browning DF,2005 supposed that Fis block access of RNAP to the nrf promoter.

6The maximum nrfA expression is achieved at low nitrate concentrations through NarP and mainly through NarL. Wang and Gunsalus Wang H,2000 reported that the nitrite is a less effective inductor of nrfA expression, although in a earlier report Page et al. 2173895 reported that this molecule was the primary signal. The sites at -70 and -79 are recognized by NarL and NarP, but NarL has the highest affinity for them.

nrf expression is increased in response to nitrite or nitrate ions by NarL or NarP. FNR and NarL/NarP act by promoting open complex formation by RNAP at the nrf promoter. Although it seems that NarL and FNR can bind to their targets independently, NarL is unable to activate the nrf promoter in the absence of FNR Browning DF,2005. NarL and IHF cannot bind together; the other protein regulators can bind together to form ternary complexes. Fis binds independently of FNR and IHF. Browning DF,2005 supposed that Fis blocks access of RNAP to the nrf promoter.
8IHF binding to a site located -55 bp from the promoter weakly represses the nrfAp promoter and strongly represses acsP1, a promoter that overlaps and is divergent to nrfAp.
NarL and IHF cannot bind together, contrary to other protein regulators that can bind together to form ternary complexes. Fis binds independently to FNR and IHF. Browning DF,2005 supposes that Fis blocks access of RNAP to the nrf promoter. Based on DNase footprinting Browning DF,2005 it is suggested that IHF alters the binding of FNR without displacing it from its site. In addition, NarL binding prevents IHF binding but has little or no effect on FNR or Fis binding. Either Fis or IHF at -55 can repress FNR-dependent open complex formation. NarL binding to its target reverses IHF-dependent repression but does not relieve Fis-dependent repression Browning DF,2005

9At low levels of nitrate, NarL activates nrfA expression and at high levels of nitrate NarL represses it.
10At low levels of nitrate, NarL activates nrfA expression and at high levels of nitrate NarL represses it.
11nrf regulation is totally dependent on FNR at this site (-41.5) under anaerobic conditions. FNR and NarL/NarP act by promoting the open complex formation by RNA polymerase at the nrf promoter. Although it seems that NarL and FNR can bind to their targets independently, NarL is unable to activate the nrf promoter in the absence of FNR Browning DF,2005. Based on DNase I footprinting Browning DF,2005 suggest that IHF alters the binding of FNR without displacing it from its site. In adittion, NarL binding prevents IHF binding but has little or no effect on FNR or Fis binding.
12The -22 and -50 NarL sites are needed for optimal repression of nrfA expression. At high nitrate concentrations NarL can repress nrfA expression, but NarP cannot Wang H,2000
13Fis binding to this site weakly represses the nrfAp promoter and strongly represses acsP1, a promoter that overlaps and is divergent to nrfAp.
Either IHF or Fis can repress FNR-dependent open complex formation. NarL binding to its target reverses IHF-dependent repression but does not relieve Fis-dependent repression Browning DF,2005.
14The regulatory effect of FlhDC in nrfA operon transcription has been proved only by microarray analysis by Pruss BM,2001.


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -9.6 4287726 4287744 aataaaaaccGCCATTGCAACAATGGCGcaattcggat
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"


Evidence    

 [IMP] Inferred from mutant phenotype

 [TIM] Transcription initiation mapping

 [BCE] Binding of cellular extracts

 [BPP] Binding of purified proteins

 [CV(CHIP-SV/GEA/ROMA)] cross validation(CHIP-SV/GEA/ROMA)

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

 [GEA] Gene expression analysis

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [CV(CHIP-SV/SM)] cross validation(CHIP-SV/SM)

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

 [SM] Site mutation

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


Reference(s)    

 [1] Hussain H., Grove J., Griffiths L., Busby S., Cole J., 1994, A seven-gene operon essential for formate-dependent nitrite reduction to ammonia by enteric bacteria., Mol Microbiol 12(1):153-63

 [2] Darwin A., Hussain H., Griffiths L., Grove J., Sambongi Y., Busby S., Cole J., 1993, Regulation and sequence of the structural gene for cytochrome c552 from Escherichia coli: not a hexahaem but a 50 kDa tetrahaem nitrite reductase., Mol Microbiol 9(6):1255-65

 [3] Tyson KL., Cole JA., Busby SJ., 1994, Nitrite and nitrate regulation at the promoters of two Escherichia coli operons encoding nitrite reductase: identification of common target heptamers for both NarP- and NarL-dependent regulation., Mol Microbiol 13(6):1045-55

 [4] Browning DF., Beatty CM., Sanstad EA., Gunn KE., Busby SJ., Wolfe AJ., 2004, Modulation of CRP-dependent transcription at the Escherichia coli acsP2 promoter by nucleoprotein complexes: anti-activation by the nucleoid proteins FIS and IHF., Mol Microbiol 51(1):241-54

 [5] Browning DF., Lee DJ., Wolfe AJ., Cole JA., Busby SJ., 2006, The Escherichia coli K-12 NarL and NarP proteins insulate the nrf promoter from the effects of integration host factor., J Bacteriol 188(21):7449-56

 [6] Sclavi B., Beatty CM., Thach DS., Fredericks CE., Buckle M., Wolfe AJ., 2007, The multiple roles of CRP at the complex acs promoter depend on activation region 2 and IHF., Mol Microbiol 65(2):425-40

 [7] Filenko N., Spiro S., Browning DF., Squire D., Overton TW., Cole J., Constantinidou C., 2007, The NsrR regulon of Escherichia coli K-12 includes genes encoding the hybrid cluster protein and the periplasmic, respiratory nitrite reductase., J Bacteriol 189(12):4410-7

 [8] Partridge JD., Bodenmiller DM., Humphrys MS., Spiro S., 2009, NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility., Mol Microbiol 73(4):680-94

 [9] Browning DF., Beatty CM., Wolfe AJ., Cole JA., Busby SJ., 2002, Independent regulation of the divergent Escherichia coli nrfA and acsP1 promoters by a nucleoprotein assembly at a shared regulatory region., Mol Microbiol 43(3):687-701

 [10] Browning DF., Grainger DC., Beatty CM., Wolfe AJ., Cole JA., Busby SJ., 2005, Integration of three signals at the Escherichia coli nrf promoter: a role for Fis protein in catabolite repression., Mol Microbiol 57(2):496-510

 [11] 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

 [12] 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

 [13] Wang H., Gunsalus RP., 2000, The nrfA and nirB nitrite reductase operons in Escherichia coli are expressed differently in response to nitrate than to nitrite., J Bacteriol 182(20):5813-22

 [14] Browning DF., Lee DJ., Spiro S., Busby SJ., 2010, Down-regulation of the Escherichia coli K-12 nrf promoter by binding of the NsrR nitric oxide-sensing transcription repressor to an upstream site., J Bacteriol 192(14):3824-8

 [15] 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

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