RegulonDB

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 Oberto J, Nabti S, Jooste V, Mignot H, Rouviere-Yaniv J,2009. 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 Zhang HK, Lu H, Wang J, Liu GF, Zhou JT, Xu MY,2013.
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:	[ICWHO] [IMP] [TIM]
Reference(s):	[2] Darwin A., et al., 1993 [3] Huerta AM., et al., 2003 [4] 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)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence (Confirmed, Strong, Weak)	Reference(s)
proximal	FNR	activator	nrfAp	4287623	4287636	-41.5	gcacttacaaTTGATTAAAGACAAcattcacagt	nd	[GEA], [BCE], [BPP]	[11], [12]

[Fis,-] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence (Confirmed, Strong, Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence (Confirmed, Strong, Weak)	Reference(s)
proximal	Fis	repressor	nrfAp	4287649	4287663	-15.0	ttcacagtgtGGTTATTTGTTACACataggggcga	nd	[GEA], [BPP]	[5], [10], [11]

[FlhDC,+] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence (Confirmed, Strong, Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence (Confirmed, Strong, Weak)	Reference(s)
nd	FlhDC	activator	nrfAp	nd	nd	nd	nd	nd	[GEA], [BPP]	[16]

[IHF,+] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence (Confirmed, Strong, Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence (Confirmed, Strong, Weak)	Reference(s)
remote	IHF	activator	nrfAp	4287538	4287550	-127.0	tgattaattcTTTGAGGAACATGcagttatgca	nd	[GEA], [AIBSCS], [BPP], [SM]	[5], [6], [7]

[IHF,-] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence (Confirmed, Strong, Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence (Confirmed, Strong, Weak)	Reference(s)
proximal	IHF	repressor	nrfAp	4287610	4287622	-55.0	tggtattttaCATGCACTTACAAttgattaaag	nd	[GEA], [BPP]	[5], [10], [11]

[NarL,+] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence (Confirmed, Strong, Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence (Confirmed, Strong, Weak)	Reference(s)
proximal	NarL-phosphorylated	activator	nrfAp	4287589	4287595	-79.0	agatactgacTAACTCTaaagtggtat	nd	[GEA], [AIBSCS], [BPP], [SM]	[4], [10], [11], [12], [13], [14]
proximal	NarL-phosphorylated	activator	nrfAp	4287598	4287604	-70.0	ctaactctaaAGTGGTAttttacatgc	nd	[GEA], [APIORCISFBSCS], [BPP], [SM]	[4], [10], [11], [12], [13], [14]
proximal	NarL-phosphorylated	activator	nrfAp	4287618	4287624	-50.0	tacatgcactTACAATTgattaaagac	nd	[GEA], [APIORCISFBSCS], [BPP], [SM]	[4], [10], [12], [13], [14]

[NarL,-] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence (Confirmed, Strong, Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence (Confirmed, Strong, Weak)	Reference(s)
proximal	NarL-phosphorylated	repressor	nrfAp	4287618	4287624	-50.0	tacatgcactTACAATTgattaaagac	nd	[GEA], [APIORCISFBSCS], [BPP], [SM]	[4], [10], [12], [13], [14]
proximal	NarL-phosphorylated	repressor	nrfAp	4287646	4287652	-22.0	acattcacagTGTGGTTatttgttaca	nd	[GEA], [APIORCISFBSCS], [BPP], [SM]	[4], [10], [12], [13], [14]

[NarP,+] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence (Confirmed, Strong, Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence (Confirmed, Strong, Weak)	Reference(s)
proximal	NarP-phosphorylated	activator	nrfAp	4287584	4287599	-79.0	gaggaagataCTGACTAACTCTAAAGtggtatttta	nd	[GEA], [APIORCISFBSCS], [BPP], [SM]	[4], [10], [11], [12], [13], [14]
proximal	NarP-phosphorylated	activator	nrfAp	4287593	4287608	-70.0	actgactaacTCTAAAGTGGTATTTTacatgcactt	nd	[GEA], [APIORCISFBSCS], [BPP], [SM]	[4], [10], [11], [12], [13], [14]

[NsrR,-] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence (Confirmed, Strong, Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence (Confirmed, Strong, Weak)	Reference(s)
remote	NsrR	repressor	nrfAp	4287545	4287556	-121.0	ttctttgaggAACATGCAGTTAtgcatgctgt	nd	[GEA], [APIORCISFBSCS]	[8], [9]
proximal	NsrR	repressor	nrfAp	4287599	4287617	-63.0	taactctaaaGTGGTATTTTACATGCACTtacaattgat	nd	[GEA], [APIORCISFBSCS], [BCE], [SM]	[9], [15]

Transcription factor	Function	Promoter	Binding Sites	Evidence (Confirmed, Strong, Weak)	Reference(s)
IHF	activator	nrfAp	4287538	4287550	-127.0	tgattaattcTTTGAGGAACATGcagttatgca	[GEA]	[5], [6], [7]
NsrR	repressor	nrfAp	4287545	4287556	-121.0	ttctttgaggAACATGCAGTTAtgcatgctgt	[GEA]	[8], [9]
NarP-phosphorylated	activator	nrfAp	4287584	4287599	-79.0	gaggaagataCTGACTAACTCTAAAGtggtatttta	[GEA]	[4], [10], [11], [12], [13], [14]
NarL-phosphorylated	activator	nrfAp	4287589	4287595	-79.0	agatactgacTAACTCTaaagtggtat	[GEA]	[4], [10], [11], [12], [13], [14]
NarP-phosphorylated	activator	nrfAp	4287593	4287608	-70.0	actgactaacTCTAAAGTGGTATTTTacatgcactt	[GEA]	[4], [10], [11], [12], [13], [14]
NarL-phosphorylated	activator	nrfAp	4287598	4287604	-70.0	ctaactctaaAGTGGTAttttacatgc	[GEA]	[4], [10], [11], [12], [13], [14]
NsrR	repressor	nrfAp	4287599	4287617	-63.0	taactctaaaGTGGTATTTTACATGCACTtacaattgat	[GEA]	[9], [15]
IHF	repressor	nrfAp	4287610	4287622	-55.0	tggtattttaCATGCACTTACAAttgattaaag	[GEA]	[5], [10], [11]
NarL-phosphorylated	activator	nrfAp	4287618	4287624	-50.0	tacatgcactTACAATTgattaaagac	[GEA]	[4], [10], [12], [13], [14]
NarL-phosphorylated	repressor	nrfAp	4287618	4287624	-50.0	tacatgcactTACAATTgattaaagac	[GEA]	[4], [10], [12], [13], [14]
FNR	activator	nrfAp	4287623	4287636	-41.5	gcacttacaaTTGATTAAAGACAAcattcacagt	[GEA]	[11], [12]
NarL-phosphorylated	repressor	nrfAp	4287646	4287652	-22.0	acattcacagTGTGGTTatttgttaca	[GEA]	[4], [10], [12], [13], [14]
Fis	repressor	nrfAp	4287649	4287663	-15.0	ttcacagtgtGGTTATTTGTTACACataggggcga	[GEA]	[5], [10], [11]
FlhDC	activator	nrfAp	nd	nd	nd	nd	[GEA]	[16]

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
[ICWHO] Inferred computationally without human oversight
[IMP] Inferred from mutant phenotype
[TIM] Transcription initiation mapping
[GEA] Gene expression analysis
[BCE] Binding of cellular extracts
[BPP] Binding of purified proteins
[AIBSCS] Automated inference based on similarity to consensus sequences
[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] 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
[4] 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
[5] 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
[6] 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
[7] 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
[8] 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
[9] 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
[10] 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
[11] 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
[12] 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
[13] 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
[14] 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
[15] 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
[16] 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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