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:

CRP	Weight Matrix Tractordb tool

Connectivity class

Global Regulator

Sensing Class

Using internal synthesized signals

Synonym(s):

Cap, Csm, DNA-binding transcriptional dual regulator CRP, GurB

Gene name(s):

crp

Functional conformation(s):

CRP , CRP-cyclic-AMP

Coregulator(s):

AaeR, AcrR, AdiY, AgaR, AraC, ArcA, ArgP, ArgR, AscG, BasR, BolA, BtsR, CRP, CRP-Sxy, CaiF, ChbR, ComR, CpxR, Cra, CreB, CsgD, CspA, CsqR, CusR, CytR, DcuR, DeoR, DgoR, DksA-ppGpp, DnaA, DpiA, DsdC, EbgR, EnvY, EvgA, ExuR, FNR, FadR, FeaR, FhlA, Fis, FlhDC, FliZ, FrlR, FucR, Fur, GadE, GadE-RcsB, GadW, GadX, GalR, GalS, GatR, GcvA, GlaR, GlcC, GlpR, GlrR, GntR, GutM, H-NS, HU, HdfR, HipB, HprR, HyfR, HypT, IHF, IclR, IdnR, LacI, LeuO, LexA, LrhA, Lrp, LsrR, MalI, MalT, MarA, MarR, MatA, McbR, MelR, MetJ, MhpR, Mlc, MlrA, ModE, MprA, MqsA, MurR, Nac, NadR, NagC, NanR, NarL, NarP, NrdR, NsrR, NtrC, OmpR, OxyR, PaaX, PdhR, PhoB, PhoP, PlaR, PrpR, PurR, PuuR, QseB, RbsR, RcdA, RcsAB, RcsB, RcsB-BglJ, RhaR, RhaS, Rob, RspR, RstA, SdiA, SlyA, SoxR, SoxS, SrlR, StpA, TdcA, TdcR, TorR, TreR, UhpA, UidR, UlaR, UvrY, UxuR, XylR, YdeO, YjjQ, ZraR, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

ArcA	Weight Matrix Tractordb tool

Connectivity class

Global Regulator

Sensing Class

External-Two-component systems

Synonym(s):

ArcA response regulator, CpxC, DNA-binding transcriptional dual regulator ArcA, Dye, FexA, Msp, Seg, SfrA, dye resistance protein

Gene name(s):

arcA

Functional conformation(s):

ArcA-phosphorylated , ArcA

Coregulator(s):

AdiY, AppY, ArcA, BetI, BtsR, CRP, CadC, CaiF, Cra, CusR, CysB, DcuR, DksA-ppGpp, DnaA, DpiA, FNR, FadR, Fis, FlhDC, Fur, GadE, GadE-RcsB, GadW, GadX, GatR, GlcC, GlpR, H-NS, HipB, HprR, HypT, IHF, IclR, IscR, LexA, LldR, Lrp, MarA, McbR, Mlc, ModE, MqsA, NarL, NarP, NsrR, NtrC, OmpR, PdhR, PhoP, PuuR, RcdA, RcsB, RhaS, Rob, RutR, SdiA, SlyA, SoxR, SoxS, TorR, TreR, YdeO, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

CusR	Tractordb tool

Connectivity class

Local Regulator

Sensing Class

External-Two-component systems

Synonym(s):

CusR response regulator, DNA-binding transcriptional activator CusR, YlcA

Gene name(s):

cusR

Functional conformation(s):

CusR , CusR-phosphorylated

Coregulator(s):

ArcA, CRP, Cra, CusR, FNR, Fis, Fur, GadE, HprR, PdhR, PhoB

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

GadE	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Synonym(s):

DNA-binding transcriptional activator GadE, YhiE, YhiT, acid-responsive regulator of gadA and gadBC

Gene name(s):

gadE

Functional conformation(s):

GadE

Coregulator(s):

AdiY, ArcA, ArgR, CRP, CadC, CpxR, Cra, CusR, EvgA, FNR, Fis, FliZ, Fur, GadE, GadE-RcsB, GadW, GadX, H-NS, HdfR, HprR, IHF, Lrp, MarA, MatA, Nac, NsrR, OmpR, PdhR, PhoB, PhoP, PurR, RcsAB, RcsB, Rob, RutR, TorR, YdeO, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

PdhR	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Sensing Class

Using internal synthesized signals

Synonym(s):

AceC, DNA-binding transcriptional dual regulator PdhR, GenA, YacB

Gene name(s):

pdhR

Functional conformation(s):

PdhR-pyruvate , PdhR

Coregulator(s):

ArcA, BasR, BtsR, CRP, CpxR, Cra, CusR, FNR, Fis, Fur, GadE, GlcC, HprR, HypT, IHF, MraZ, NsrR, OxyR, PdhR, PhoP

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

Cra	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Sensing Class

Using internal synthesized signals

Synonym(s):

DNA-binding transcriptional dual regulator Cra, FruC, FruR, Shl

Gene name(s):

cra

Functional conformation(s):

Cra-beta;-D-fructose 1,6-bisphosphate , Cra , Cra-β-D-fructofuranose 1-phosphate

Coregulator(s):

AcrR, ArcA, BasR, BetI, BolA, BtsR, CRP, CpxR, Cra, CsgD, CusR, DcuR, DksA, FNR, Fis, FliZ, Fur, GadE, GlcC, GntR, H-NS, HprR, IHF, IclR, KdgR, Lrp, MarA, MarR, Mlc, MlrA, MqsA, NagC, NarL, NarP, OmpR, PdhR, PrpR, RcdA, RcsAB, Rob, RstA, SgrR, SoxS, TyrR, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

HprR	Tractordb tool

Connectivity class

Local Regulator

Sensing Class

External-Two-component systems

Synonym(s):

DNA-binding transcriptional dual regulator HprR, YedW

Gene name(s):

hprR

Functional conformation(s):

HprR-phosphorylated , HprR

Coregulator(s):

ArcA, CRP, Cra, CusR, FNR, Fis, Fur, GadE, HprR, PdhR, PhoB

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

Fur	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Sensing Class

External sensing using transported metabolites

Synonym(s):

DNA-binding transcriptional dual regulator Fur

Gene name(s):

fur

Functional conformation(s):

Fur-Fe²⁺ , Fur , Fur-Mn²⁺

Coregulator(s):

AcrR, AdiY, ArcA, ArgP, ArgR, CRP, CdaR, CpxR, Cra, CusR, EnvY, FNR, Fis, FliZ, Fur, GadE, GadX, H-NS, HdfR, HprR, HypT, IHF, IscR, LrhA, Lrp, MarA, MatA, MetR, MntR, ModE, MqsA, Nac, NagC, NarL, NfeR, NrdR, NsrR, NtrC, OmpR, OxyR, PdhR, PhoB, PurR, QseB, RcnR, RcsAB, Rob, RstA, RutR, SlyA, SoxR, SoxS, YjjQ, Zur, ppGpp

Summary:

TF Summary ...[more]

REGULATION EXERTED BY ArcA,CRP,Cra,CusR,FNR,Fis,Fur,GadE,HprR,PdhR

Info M3D | Colombos

KNOWN BINDING SITES (The central relative position is relative to the promoter +1)
ArcA repressor CRP activator Cra repressor CusR activator FNR repressor Fis activator Fur repressor GadE activator HprR repressor PdhR repressor
Transcription Factor		Regulated		Binding Sites				Evidence	References
Functional conformation	Function	Promoter	Gene(s)	LeftPos	RigthPos	Central Rel-Pos	Sequence
CRP-cyclic-AMP	activator	cyoAp	cyoE , cyoD , cyoC , cyoB , cyoA	451680	451701	-37.5	caagtaacagGAATTTAATCATGTTTACAGTAatgtaacctt	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[1]
CRP-cyclic-AMP	activator	cyoAp	cyoE , cyoD , cyoC , cyoB , cyoA	451834	451855	-191.5	tatttgttaaATAATTGTTTTATTTCACATTGgttataccaa	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[1]
ArcA-phosphorylated	repressor	cyoAp	cyoE , cyoD , cyoC , cyoB , cyoA	451846	451860	-200.0	ataattatttGTTAAATAATTGTTTtatttcacat	[EXP-IEP-GENE-EXPRESSION-ANALYSIS] [EXP-IEP-MICROARRAY]	[2] [3] [4] [5]
Fur-Fe²⁺	repressor	cyoAp	cyoE , cyoD , cyoC , cyoB , cyoA	451857	451875	-213.0	gttgtcactcTAATGATAATTATTTGTTAaataattgtt	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[6] [7]
PdhR	repressor	cyoAp	cyoE , cyoD , cyoC , cyoB , cyoA	451822	451838	-177.0	ttttatttcaCATTGGTTATACCAATTgcccgcccag	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[8]
FNR	repressor	cyoAp	cyoE , cyoD , cyoC , cyoB , cyoA	451839	451852	-192.5	ttgttaaataATTGTTTTATTTCAcattggttat	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[9] [2] [6] [10] [11]
Cra	repressor	cyoAp	cyoE , cyoD , cyoC , cyoB , cyoA	451913	451930	-268.5	aattctatttTTCTTACACGATTCAGCTaatgagtctt	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[12]
CusR-phosphorylated	activator	cyoAp	cyoE , cyoD , cyoC , cyoB , cyoA	451577	451593	69.5	tcaggaaataCAATAAAAGTTTGGGATggttgtcatt		[13]
HprR-phosphorylated	repressor	cyoAp	cyoE , cyoD , cyoC , cyoB , cyoA	451576	451594	69.5	ctcaggaaatACAATAAAAGTTTGGGATGgttgtcatta	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[13]
GadE	activator	cyoAp	cyoE , cyoD , cyoC , cyoB , cyoA

Evidence:	[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis [EXP-IEP-MICROARRAY] high throughput expression microarray evidence
Reference(s):	[1] Zheng D., et al., 2004 [2] Cotter PA., et al., 1992 [3] Federowicz S., et al., 2014 [4] Lynch AS., et al., 1996 [5] Salmon KA., et al., 2005 [6] Kumar R., et al., 2011 [7] Stojiljkovic I., et al., 1994 [8] Ogasawara H., et al., 2007 [9] Constantinidou C., et al., 2006 [10] Salmon K., et al., 2003 [11] Spiro S., et al., 1991 [12] Shimada T., et al., 2011 [13] Urano H., et al., 2015

Reference(s)
[1] Zheng D., Constantinidou C., Hobman JL., Minchin SD., 2004, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling., Nucleic Acids Res 32(19):5874-93
[2] Cotter PA., Gunsalus RP., 1992, Contribution of the fnr and arcA gene products in coordinate regulation of cytochrome o and d oxidase (cyoABCDE and cydAB) genes in Escherichia coli., FEMS Microbiol Lett 70(1):31-6
[3] Federowicz S., Kim D., Ebrahim A., Lerman J., Nagarajan H., Cho BK., Zengler K., Palsson B., 2014, Determining the control circuitry of redox metabolism at the genome-scale., PLoS Genet 10(4):e1004264
[4] Lynch AS., Lin EC., 1996, Transcriptional control mediated by the ArcA two-component response regulator protein of Escherichia coli: characterization of DNA binding at target promoters., J Bacteriol 178(21):6238-49
[5] Salmon KA., Hung SP., Steffen NR., Krupp R., Baldi P., Hatfield GW., Gunsalus RP., 2005, Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA., J Biol Chem 280(15):15084-96
[6] Kumar R., Shimizu K., 2011, Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures., Microb Cell Fact 10:3
[7] Stojiljkovic I., Baumler AJ., Hantke K., 1994, Fur regulon in gram-negative bacteria. Identification and characterization of new iron-regulated Escherichia coli genes by a fur titration assay., J Mol Biol 236(2):531-45
[8] Ogasawara H., Ishida Y., Yamada K., Yamamoto K., Ishihama A., 2007, PdhR (pyruvate dehydrogenase complex regulator) controls the respiratory electron transport system in Escherichia coli., J Bacteriol 189(15):5534-41
[9] Constantinidou C., Hobman JL., Griffiths L., Patel MD., Penn CW., Cole JA., Overton TW., 2006, A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth., J Biol Chem 281(8):4802-15
[10] Salmon K., Hung SP., Mekjian K., Baldi P., Hatfield GW., Gunsalus RP., 2003, Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR., J Biol Chem 278(32):29837-55
[11] Spiro S., Guest JR., 1991, Adaptive responses to oxygen limitation in Escherichia coli., Trends Biochem Sci 16(8):310-4
[12] Shimada T., Yamamoto K., Ishihama A., 2011, Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli., J Bacteriol 193(3):649-59
[13] Urano H., Umezawa Y., Yamamoto K., Ishihama A., Ogasawara H., 2015, Cooperative regulation of the common target genes between H2O2-sensing YedVW and Cu2+-sensing CusSR in Escherichia coli., Microbiology 161(Pt 4):729-38
[14] Hommais F., Krin E., Coppee JY., Lacroix C., Yeramian E., Danchin A., Bertin P., 2004, GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli., Microbiology 150(Pt 1):61-72
[15] 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