RegulonDB

TRANSCRIPTION FACTOR:

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:

H-NS	Tractordb tool

Connectivity class

Global Regulator

Sensing Class

TFs for DNA-bending

Synonym(s):

BglY, Cur, DNA-binding protein HLP-II (HU, BH2, HD, NS), DNA-binding transcriptional dual regulator H-NS, Drc, DrdX, Drs, FimG, Hns, HnsA, Irk, MsyA, OsmZ, PilG, TopS, TopX, VirR

Gene name(s):

hns

Functional conformation(s):

H-NS

Coregulator(s):

AcrR, AdiY, ArcA, ArgP, ArgR, BasR, BolA, BtsR, CRP, CadC, CaiF, CdaR, CpxR, Cra, CreB, CsgD, CspA, CysB, DksA, DksA-ppGpp, DnaA, DpiA, EvgA, FNR, Fis, FlhDC, FliZ, Fur, GadE, GadE-RcsB, GadW, GadX, GalR, GalS, GlaR, GutM, H-NS, HU, HdfR, HypT, IHF, LacI, LeuO, LrhA, Lrp, MalT, MarA, MatA, McbR, MlrA, MntR, MqsA, NagC, NanR, NarL, NarP, NhaR, NrdR, NsrR, OmpR, OxyR, PhoB, PhoP, QseB, RcdA, RcsAB, RcsB, RcsB-BglJ, Rob, RstA, RutR, SdiA, SlyA, SoxS, SrlR, StpA, SutR, TorR, UvrY, YdeO, YjjQ, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

LrhA	Tractordb tool

Connectivity class

Local Regulator

Synonym(s):

DNA-binding transcriptional dual regulator LrhA, GenR

Gene name(s):

lrhA

Functional conformation(s):

LrhA

Coregulator(s):

AcrR, CRP, FliZ, Fur, H-NS, HdfR, IHF, LeuO, LrhA, Lrp, MatA, OmpR, QseB, RcsAB, SlyA, YjjQ, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

HdfR	Tractordb tool

Connectivity class

Local Regulator

Synonym(s):

DNA-binding transcriptional dual regulator HdfR, YifA, YifD

Gene name(s):

hdfR

Functional conformation(s):

HdfR

Coregulator(s):

AcrR, AdiY, ArgR, CRP, FNR, FliZ, Fur, GadE, H-NS, HdfR, IHF, LrhA, Lrp, MatA, Nac, OmpR, QseB, RcsAB, YjjQ

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

QseB	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Sensing Class

External-Two-component systems

Synonym(s):

DNA-binding transcriptional activator QseB, QseB response regulator, YgiX

Gene name(s):

qseB

Functional conformation(s):

QseB-Phosphorylated , QseB

Coregulator(s):

AcrR, BasR, CRP, FliZ, Fur, H-NS, HdfR, IHF, LrhA, Lrp, MatA, Nac, NsrR, OmpR, PhoB, QseB, RcsAB, YjjQ

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

AcrR	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Synonym(s):

DNA-binding transcriptional repressor AcrR, YbaH

Gene name(s):

acrR

Functional conformation(s):

AcrR-Proflavin , AcrR-R6G , AcrR-ethidium , AcrR

Coregulator(s):

AcrR, CRP, CpxR, Cra, EnvR, FNR, Fis, FliZ, Fur, H-NS, HU, HdfR, IHF, LrhA, Lrp, MarA, MarR, MatA, MprA, OmpR, PhoP, QseB, RcsAB, Rob, SoxR, SoxS, YjjQ

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

MatA	Tractordb tool

Connectivity class

Local Regulator

Synonym(s):

DNA-binding transcriptional dual regulator MatA, EcpR, YkgK

Gene name(s):

matA

Functional conformation(s):

MatA

Coregulator(s):

AcrR, CRP, CsgD, FlhDC, FliZ, Fur, GadE, H-NS, HdfR, IHF, LrhA, MatA, NsrR, OmpR, QseB, RcsAB, SutR, YjjQ

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

FliZ	Tractordb tool

Connectivity class

Local Regulator

Synonym(s):

DNA-binding transcriptional regulator FliZ, YedH

Gene name(s):

fliZ

Functional conformation(s):

FliZ

Coregulator(s):

AcrR, AdiY, BasR, BolA, BtsR, CRP, CpxR, Cra, CsgD, EvgA, Fis, FliZ, Fur, GadE, GadW, GadX, H-NS, HdfR, IHF, LrhA, Lrp, MarA, MatA, MlrA, MqsA, OmpR, PhoP, QseB, RcdA, RcsAB, RcsB, RstA, RutR, TorR, YdeO, YjjQ, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

YjjQ	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Synonym(s):

DNA-binding transcriptional repressor YjjQ

Gene name(s):

yjjQ

Functional conformation(s):

YjjQ

Coregulator(s):

AcrR, CRP, CpxR, EnvY, FliZ, Fur, H-NS, HdfR, IHF, LrhA, Lrp, MatA, OmpR, QseB, RcsAB, YjjQ

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:

RcsAB

Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Synonym(s):

RcsAB DNA-binding transcriptional dual regulator

Gene name(s):

rcsA, rcsB

Functional conformation(s):

RcsAB

Coregulator(s):

AcrR, BasR, BolA, BtsR, CRP, CpxR, Cra, CsgD, FliZ, Fur, GadE, H-NS, HdfR, IHF, LrhA, MatA, MlrA, MqsA, OmpR, QseB, RcdA, RcsAB, RstA, YjjQ, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

OmpR	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Sensing Class

External-Two-component systems

Synonym(s):

Cry, DNA-binding transcriptional dual regulator OmpR, Kmt, OmpB, OmpR response regulator

Gene name(s):

ompR

Functional conformation(s):

OmpR-phosphorylated , OmpR

Coregulator(s):

AcrR, ArcA, BasR, BolA, BtsR, CRP, CadC, CpxR, Cra, CsgD, EnvY, FNR, FadR, Fis, FliZ, Fur, GadE-RcsB, GadX, H-NS, HU, HdfR, IHF, LeuO, LrhA, Lrp, MarA, MatA, MlrA, MprA, MqsA, NagC, NhaR, OmpR, PhoB, PhoP, QseB, RcdA, RcsAB, Rob, RstA, SoxS, YjjQ, ppGpp

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 AcrR,CRP,FliZ,Fur,H-NS,HdfR,IHF,LrhA,MatA,OmpR,QseB,RcsAB,YjjQ

Info M3D | Colombos

KNOWN BINDING SITES (The central relative position is relative to the promoter +1)
AcrR repressor CRP activator FliZ repressor Fur repressor H-NS activator HdfR repressor IHF repressor LrhA repressor MatA repressor OmpR repressor QseB activator RcsAB repressor YjjQ repressor
Transcription Factor		Regulated		Binding Sites				Evidence	References
Functional conformation	Function	Promoter	Gene(s)	LeftPos	RigthPos	Central Rel-Pos	Sequence
CRP-cyclic-AMP	activator	flhDp	flhC , flhD	1978456	1978477	-71.5	attgagtgttTTGTGTGATCTGCATCACGCATtattgaaaat	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[1] [2] [3]
IHF	repressor	flhDp	flhC , flhD	1978481	1978493	-92.0	ccatttatgtTAAGTAATTGAGTgttttgtgtg		[4]
LrhA	repressor	flhDp	flhC , flhD	1978500	1978514	-112.0	tcaataagttGGAGTCATTACCCATttatgttaag	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[5]
OmpR-phosphorylated	repressor	flhDp	flhC , flhD	1978531	1978550	-145.5	caaagtcatcGGGCATTATCTGAACATAAAacactatcaa
OmpR-phosphorylated	repressor	flhDp	flhC , flhD	1978368	1978387	18.5	tcgatttaggAAAAATCTTAGATAAGTGTAaagacccatt
Fur-Fe²⁺	repressor	flhDp	flhC , flhD	1978272	1978290	115.0	caactattctAATGCTAATTATTTTTTACcggggcttcc		[6]
YjjQ	repressor	flhDp	flhC , flhD	1978378	1978392	11.0	ttgcgtcgatTTAGGAAAAATCTTAgataagtgta	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[7]
AcrR	repressor	flhDp	flhC , flhD	1978422	1978432	-31.5	agcccccctcCGTTGTATGTGcgtgtagtga	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[8]
H-NS	activator	flhDp	flhC , flhD

Evidence:	[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
Reference(s):	[1] Amores GR., et al., 2017 [2] Otsuka J., et al., 1996 [3] Soutourina O., et al., 1999 [4] Shin S., et al., 1995 [5] Lehnen D., et al., 2002 [6] Stojiljkovic I., et al., 1994 [7] Wiebe H., et al., 2015 [8] Kim YJ., et al., 2016

Reference(s)
[1] Amores GR., de Las Heras A., Sanches-Medeiros A., Elfick A., Silva-Rocha R., 2017, Systematic identification of novel regulatory interactions controlling biofilm formation in the bacterium Escherichia coli., Sci Rep 7(1):16768
[2] Otsuka J., Watanabe H., Mori KT., 1996, Evolution of transcriptional regulation system through promiscuous coupling of regulatory proteins with operons; suggestion from protein sequence similarities in Escherichia coli., J Theor Biol 178(2):183-204
[3] Soutourina O., Kolb A., Krin E., Laurent-Winter C., Rimsky S., Danchin A., Bertin P., 1999, Multiple control of flagellum biosynthesis in Escherichia coli: role of H-NS protein and the cyclic AMP-catabolite activator protein complex in transcription of the flhDC master operon., J Bacteriol 181(24):7500-8
[4] Shin S., Park C., 1995, Modulation of flagellar expression in Escherichia coli by acetyl phosphate and the osmoregulator OmpR., J Bacteriol 177(16):4696-702
[5] Lehnen D., Blumer C., Polen T., Wackwitz B., Wendisch VF., Unden G., 2002, LrhA as a new transcriptional key regulator of flagella, motility and chemotaxis genes in Escherichia coli., Mol Microbiol 45(2):521-32
[6] 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
[7] Wiebe H., Gurlebeck D., Gross J., Dreck K., Pannen D., Ewers C., Wieler LH., Schnetz K., 2015, YjjQ Represses Transcription of flhDC and Additional Loci in Escherichia coli., J Bacteriol 197(16):2713-20
[8] Kim YJ., Im SY., Lee JO., Kim OB., 2016, Potential Swimming Motility Variation by AcrR in Escherichia coli., J Microbiol Biotechnol 26(10):1824-1828
[9] Pesavento C., Hengge R., 2012, The global repressor FliZ antagonizes gene expression by σS-containing RNA polymerase due to overlapping DNA binding specificity., Nucleic Acids Res 40(11):4783-93
[10] Lehti TA., Bauchart P., Dobrindt U., Korhonen TK., Westerlund-Wikstrom B., 2012, The fimbriae activator MatA switches off motility in Escherichia coli by repression of the flagellar master operon flhDC., Microbiology 158(Pt 6):1444-55
[11] Ko M., Park C., 2000, H-NS-Dependent regulation of flagellar synthesis is mediated by a LysR family protein., J Bacteriol 182(16):4670-2
[12] Filippova EV., Zemaitaitis B., Aung T., Wolfe AJ., Anderson WF., 2018, Structural Basis for DNA Recognition by the Two-Component Response Regulator RcsB., MBio 9(1)
[13] Francez-Charlot A., Laugel B., Van Gemert A., Dubarry N., Wiorowski F., Castani?-Cornet MP., Gutierrez C., Cam K., 2003, RcsCDB His-Asp phosphorelay system negatively regulates the flhDC operon in Escherichia coli., Mol Microbiol 49(3):823-32
[14] Sperandio V., Torres AG., Kaper JB., 2002, Quorum sensing Escherichia coli regulators B and C (QseBC): a novel two-component regulatory system involved in the regulation of flagella and motility by quorum sensing in E. coli., Mol Microbiol 43(3):809-21