RegulonDB

TRANSCRIPTION FACTOR:

Name:

Fis	Weight Matrix Tractordb tool

Connectivity class

Global Regulator

Sensing Class

TFs for DNA-bending

Synonym(s):

DNA-binding transcriptional dual regulator Fis, Nbp, site-specific DNA inversion stimulation factor

Gene name(s):

fis

Functional conformation(s):

Fis

Coregulator(s):

AcrR, AdiY, AppY, ArcA, ArgP, BasR, CRP, CpxR, Cra, CreB, CspA, CusR, CytR, DeoR, DksA, DksA-ppGpp, DnaA, FNR, FadR, Fis, FlhDC, FliZ, Fur, GadE, GadE-RcsB, GadW, GadX, GlcC, GlpR, H-NS, HprR, IHF, IscR, LeuO, Lrp, MalT, MarA, MarR, MazE, MazE-MazF, Mlc, MntR, ModE, NanR, NarL, NarP, NrdR, NsrR, NtrC, OmpR, OxyR, PdhR, PepA, PurR, RcsB, RcsB-BglJ, Rob, RstA, RutR, SlyA, SoxS, StpA, TorR, XylR, YdeO, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

FNR	Weight Matrix Tractordb tool

Connectivity class

Global Regulator

Sensing Class

Using internal synthesized signals

Synonym(s):

DNA-binding transcriptional dual regulator FNR, NirA, NirR, OssA, OxrA

Gene name(s):

fnr

Functional conformation(s):

FNR , FNR-[4Fe-4S]²⁺ reduced , FNR-[2Fe-2S]²⁺ oxidized

Coregulator(s):

AcrR, AdiY, ArcA, ArgP, ArgR, BtsR, CRP, CadC, CaiF, Cbl, CdaR, Cra, CueR, CusR, CysB, DcuR, DksA, DksA-ppGpp, DnaA, DpiA, EvgA, ExuR, FNR, FhlA, Fis, FlhDC, Fur, GadE, GadE-RcsB, GadW, GadX, GcvA, GlpR, H-NS, HdfR, HprR, HyfR, HypT, IHF, LeuO, Lrp, MalT, MarA, MetR, MlrA, ModE, Nac, NagC, NarL, NarP, NfeR, NikR, NorR, NrdR, NsrR, NtrC, OmpR, OxyR, PdhR, PhoB, PhoP, PurR, PuuR, RcsB, Rob, RstA, RutR, SlyA, SoxR, SoxS, TdcA, TdcR, TorR, YeiL, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

NarL	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Sensing Class

External-Two-component systems

Synonym(s):

DNA-binding transcriptional dual regulator NarL, FrdR, NarR, nitrate/nitrite response regulator NarL

Gene name(s):

narL

Functional conformation(s):

NarL-phosphorylated , NarL

Coregulator(s):

AppY, ArcA, CRP, Cra, DcuR, DpiA, EvgA, FNR, FhlA, Fis, FlhDC, Fur, H-NS, IHF, IscR, Lrp, ModE, NagC, NarL, NarP, NikR, NorR, NsrR, OxyR, PhoP, RcsB, RstA, SoxS, TorR, UvrY, YdeO

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

NarP	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Sensing Class

External-Two-component systems

Synonym(s):

DNA-binding transcriptional dual regulator NarP, nitrate/nitrite response regulator NarP

Gene name(s):

narP

Functional conformation(s):

NarP-phosphorylated , NarP

Coregulator(s):

AppY, ArcA, CRP, Cra, EvgA, FNR, FhlA, Fis, FlhDC, H-NS, IHF, IscR, ModE, NagC, NarL, NarP, NorR, NsrR, OxyR, PhoP, RcsB, UvrY, YdeO

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

NsrR	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Synonym(s):

DNA-binding transcriptional regulator NsrR, YjeB

Gene name(s):

nsrR

Functional conformation(s):

NsrR-nitric oxide , NsrR , NsrR-[2Fe-2S]reduced , NsrR-[2Fe-2S]²⁺ oxidized

Coregulator(s):

ArcA, CRP, CpxR, CsgD, CytR, DksA, DksA-ppGpp, DsdC, FNR, FeaR, FhlA, Fis, FlhDC, Fur, GadE, H-NS, IHF, IscR, Lrp, MatA, MetR, ModE, Nac, NarL, NarP, NorR, NsrR, OxyR, PdhR, PhoB, QseB, SutR, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

IHF	Weight Matrix Tractordb tool

Connectivity class

Global Regulator

Sensing Class

TFs for DNA-bending

Synonym(s):

DNA-binding transcriptional dual regulator IHF

Gene name(s):

ihfB, ihfA

Functional conformation(s):

IHF

Coregulator(s):

AcrR, AdiY, ArcA, ArgR, AtoC, BasR, BolA, BtsR, CRP, Cbl, CpxR, Cra, CsgD, CysB, DksA, DksA-ppGpp, EnvY, FNR, FadR, FhlA, Fis, FlhDC, FliZ, Fur, GadE, GlcC, GlpR, GlrR, H-NS, HU, HdfR, HipAB, HipB, IHF, IclR, IscR, LrhA, Lrp, MarA, MatA, MlrA, MntR, ModE, MprA, MqsA, Nac, NagC, NanR, NarL, NarP, NorR, NsrR, NtrC, OmpR, OxyR, PaaX, PdhR, PepA, PhoB, PlaR, PspF, PurR, QseB, RcdA, RcsAB, Rob, RstA, RtcR, RutR, SlyA, SoxR, SoxS, SutR, TdcA, TdcR, TrpR, TyrR, UlaR, UvrY, YeiL, YjjQ, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

FlhDC

Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Synonym(s):

FlhDC DNA-binding transcriptional dual regulator

Gene name(s):

flhC, flhD

Functional conformation(s):

FlhDC

Coregulator(s):

ArcA, BtsR, CRP, CsgD, DpiA, FNR, FhlA, Fis, FlhDC, GalR, GalS, GlpR, H-NS, IHF, MatA, ModE, NarL, NarP, NsrR, PdeL, SutR

Summary:

TF Summary ...[more]

REGULATION EXERTED BY FNR,Fis,FlhDC,IHF,NarL,NarP,NsrR

Info M3D | Colombos

KNOWN BINDING SITES (The central relative position is relative to the promoter +1)
FNR activator Fis repressor FlhDC activator IHF dual NarL dual NarP activator NsrR repressor
Transcription Factor		Regulated		Binding Sites				Evidence	References
Functional conformation	Function	Promoter	Gene(s)	LeftPos	RigthPos	Central Rel-Pos	Sequence
IHF	activator	nrfAp	nrfA , nrfB , nrfC , nrfD , nrfE , nrfF , nrfG	4287538	4287550	-127.0	tgattaattcTTTGAGGAACATGcagttatgca	[GEA]	[1] [2] [3]
NarP-phosphorylated	activator	nrfAp	nrfA , nrfB , nrfC , nrfD , nrfE , nrfF , nrfG	4287584	4287599	-79.0	gaggaagataCTGACTAACTCTAAAGtggtatttta	[GEA]	[4] [5] [6] [7] [8] [9]
NarP-phosphorylated	activator	nrfAp	nrfA , nrfB , nrfC , nrfD , nrfE , nrfF , nrfG	4287593	4287608	-70.0	actgactaacTCTAAAGTGGTATTTTacatgcactt	[GEA]	[4] [5] [6] [7] [8] [9]
NarL-phosphorylated	activator	nrfAp	nrfA , nrfB , nrfC , nrfD , nrfE , nrfF , nrfG	4287618	4287624	-50.0	tacatgcactTACAATTgattaaagac	[GEA]	[4] [6] [7] [8] [9]
IHF	repressor	nrfAp	nrfA , nrfB , nrfC , nrfD , nrfE , nrfF , nrfG	4287610	4287622	-55.0	tggtattttaCATGCACTTACAAttgattaaag	[GEA]	[1] [4] [5]
NarL-phosphorylated	repressor	nrfAp	nrfA , nrfB , nrfC , nrfD , nrfE , nrfF , nrfG	4287646	4287652	-22.0	acattcacagTGTGGTTatttgttaca	[GEA]	[4] [6] [7] [8] [9]
Fis	repressor	nrfAp	nrfA , nrfB , nrfC , nrfD , nrfE , nrfF , nrfG	4287649	4287663	-15.0	ttcacagtgtGGTTATTTGTTACACataggggcga	[GEA]	[1] [4] [5]
FNR	activator	nrfAp	nrfA , nrfB , nrfC , nrfD , nrfE , nrfF , nrfG	4287623	4287636	-41.5	gcacttacaaTTGATTAAAGACAAcattcacagt	[GEA]	[5] [6]
NsrR	repressor	nrfAp	nrfA , nrfB , nrfC , nrfD , nrfE , nrfF , nrfG	4287545	4287556	-121.0	ttctttgaggAACATGCAGTTAtgcatgctgt	[GEA]	[10] [11]
NarL-phosphorylated	repressor	nrfAp	nrfA , nrfB , nrfC , nrfD , nrfE , nrfF , nrfG	4287618	4287624	-50.0	tacatgcactTACAATTgattaaagac	[GEA]	[4] [6] [7] [8] [9]
NarL-phosphorylated	activator	nrfAp	nrfA , nrfB , nrfC , nrfD , nrfE , nrfF , nrfG	4287598	4287604	-70.0	ctaactctaaAGTGGTAttttacatgc	[GEA]	[4] [5] [6] [7] [8] [9]
FlhDC	activator	nrfAp	nrfA , nrfB , nrfC , nrfD , nrfE , nrfF , nrfG

Evidence:	[GEA] Gene expression analysis
Reference(s):	[1] Browning DF., et al., 2004 [2] Browning DF., et al., 2006 [3] Sclavi B., et al., 2007 [4] Browning DF., et al., 2002 [5] Browning DF., et al., 2005 [6] Darwin AJ., et al., 1997 [7] Rabin RS., et al., 1993 [8] Tyson KL., et al., 1994 [9] Wang H., et al., 2000 [10] Filenko N., et al., 2007 [11] Partridge JD., et al., 2009

Reference(s)
[1] 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
[2] 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
[3] 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
[4] 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
[5] 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
[6] 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
[7] 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
[8] 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
[9] 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
[10] 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
[11] 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
[12] 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
[13] 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