RegulonDB

TRANSCRIPTION FACTOR:

Name:

CpxR	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Sensing Class

External-Two-component systems

Synonym(s):

CpxR response regulator, DNA-binding transcriptional dual regulator CpxR, YiiA

Gene name(s):

cpxR

Functional conformation(s):

CpxR-phosphorylated , CpxR

Coregulator(s):

AcrR, BaeR, BasR, BolA, BtsR, CRP, CpxR, Cra, CsgD, CysB, EnvY, Fis, FliZ, Fur, GadE, H-NS, IHF, Lrp, MarA, MarR, MlrA, MqsA, NsrR, OmpR, PdhR, PhoB, RcdA, RcsAB, RcsB, Rob, RstA, SoxS, TyrR, YjjQ, 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-cyclic-AMP , CRP

Coregulator(s):

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, RstA, SdiA, SlyA, SoxR, SoxS, SrlR, StpA, TdcA, TdcR, TorR, TreR, UhpA, UidR, UlaR, UvrY, UxuR, XylR, YdeO, YjjQ, ZraR, ppGpp

Summary:

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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:

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-β-D-fructofuranose 1-phosphate , Cra

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:

CsgD	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Synonym(s):

DNA-binding transcriptional dual regulator CsgD

Gene name(s):

csgD

Functional conformation(s):

CsgD

Coregulator(s):

BasR, BolA, BtsR, CRP, CpxR, Cra, CsgD, DksA-ppGpp, FlhDC, FliZ, H-NS, IHF, MatA, MlrA, MqsA, NsrR, OmpR, PdeL, RcdA, RcsAB, RstA, SutR, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

BolA	Tractordb tool

Connectivity class

Local Regulator

Sensing Class

External-Two-component systems

Synonym(s):

DNA-binding transcriptional dual regulator BolA

Gene name(s):

bolA

Functional conformation(s):

BolA-phosphorylated

Coregulator(s):

BasR, BolA, BtsR, CRP, CpxR, Cra, CsgD, FliZ, H-NS, IHF, MlrA, MqsA, OmpR, RcdA, RcsAB, RstA, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

RstA	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Sensing Class

External-Two-component systems

Synonym(s):

DNA-binding transcriptional regulator RstA, RstA response regulator, UrpT

Gene name(s):

rstA

Functional conformation(s):

RstA-phosphorylated , RstA

Coregulator(s):

BasR, BolA, BtsR, CRP, CpxR, Cra, CsgD, EnvY, FNR, Fis, FliZ, Fur, H-NS, IHF, MlrA, MqsA, NarL, OmpR, PhoB, RcdA, RcsAB, RstA, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

MqsA	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Synonym(s):

YgiT, antitoxin of the MqsRA toxin-antitoxin system / DNA-binding transcriptional repressor MqsA

Gene name(s):

mqsA

Functional conformation(s):

MqsA

Coregulator(s):

ArcA, BasR, BolA, BtsR, CRP, CpxR, Cra, CsgD, FliZ, Fur, GadX, H-NS, IHF, MlrA, MqsA, OmpR, RcdA, RcsAB, RstA, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

MlrA	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Synonym(s):

DNA-binding transcriptional activator MlrA, YehV

Gene name(s):

mlrA

Functional conformation(s):

MlrA

Coregulator(s):

BasR, BolA, BtsR, CRP, CadC, CpxR, Cra, CsgD, DksA-ppGpp, FNR, FliZ, H-NS, IHF, LeuO, MlrA, MqsA, OmpR, RcdA, RcsAB, RstA, ppGpp

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:

BtsR	Tractordb tool

Connectivity class

Local Regulator

Sensing Class

External-Two-component systems

Synonym(s):

DNA-binding transcriptional dual regulator BtsR, YehT

Gene name(s):

btsR

Functional conformation(s):

BtsR-Phosphorylated , BtsR

Coregulator(s):

ArcA, BasR, BolA, BtsR, CRP, CpxR, Cra, CsgD, DpiA, FNR, FlhDC, FliZ, H-NS, IHF, MlrA, MqsA, OmpR, PdhR, RcdA, RcsAB, RstA, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

BasR	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Sensing Class

External-Two-component systems

Synonym(s):

BasR response regulator, DNA-binding transcriptional dual regulator BasR, PmrA

Gene name(s):

basR

Functional conformation(s):

BasR , BasR-phosphorylated

Coregulator(s):

BasR, BolA, BtsR, CRP, CpxR, Cra, CsgD, DksA, DksA-ppGpp, Fis, FliZ, H-NS, IHF, MarA, MlrA, MqsA, NagC, NanR, OmpR, PdhR, PhoP, PutA, QseB, RcdA, RcsAB, RstA, SoxR, SoxS, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

RcdA	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Synonym(s):

DNA-binding transcriptional regulator RcdA, YbjK

Gene name(s):

rcdA

Functional conformation(s):

RcdA

Coregulator(s):

ArcA, BasR, BolA, BtsR, CRP, CpxR, Cra, CsgD, FliZ, H-NS, IHF, LexA, McbR, MlrA, MqsA, OmpR, PhoB, RcdA, RcsAB, RstA, SdiA, SlyA, 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:

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 , OmpR-phosphorylated

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

REGULATION EXERTED BY BasR,BolA,BtsR,CRP,CpxR,Cra,CsgD,FliZ,H-NS,IHF,MlrA,MqsA,OmpR,RcdA,RcsAB,RstA,ppGpp

Info M3D | Colombos

KNOWN BINDING SITES (The central relative position is relative to the promoter +1)
BasR activator BolA activator BtsR repressor CRP activator CpxR repressor Cra activator CsgD activator FliZ repressor H-NS repressor IHF activator MlrA activator MqsA repressor OmpR activator RcdA activator RcsAB repressor RstA repressor ppGpp activation
Transcription Factor		Regulated		Binding Sites				Evidence	References
Functional conformation	Function	Promoter	Gene(s)	LeftPos	RigthPos	Central Rel-Pos	Sequence
OmpR-phosphorylated	activator	csgDp3	csgG , csgF , csgE , csgD	1103384	1103403	-49.5	aatataacgaGTTACATTTAGTTACATGTTtaacacttga	[GEA]	[1] [2] [3]
RcdA	activator	csgDp3	csgG , csgF , csgE , csgD	1103638	1103648	-298.5	tgcgatatgtCTTGCGCACAAgccgtgacaa	[GEA] [IC]	[4]
CpxR-phosphorylated	repressor	csgDp3	csgG , csgF , csgE , csgD	1103335	1103349	3.0	tggctagattGAAATCAGATGTAATccattagttt	[GEA]	[1]
RcsAB	repressor	csgDp3	csgG , csgF , csgE , csgD

Evidence:	[GEA] Gene expression analysis [IC] Inferred by curator
Reference(s):	[1] Jubelin G., et al., 2005 [2] Ogasawara H., et al., 2010 [3] Prigent-Combaret C., et al., 2001 [4] Shimada T., et al., 2012

Reference(s)
[1] Jubelin G., Vianney A., Beloin C., Ghigo JM., Lazzaroni JC., Lejeune P., Dorel C., 2005, CpxR/OmpR interplay regulates curli gene expression in response to osmolarity in Escherichia coli., J Bacteriol 187(6):2038-49
[2] Ogasawara H., Yamada K., Kori A., Yamamoto K., Ishihama A., 2010, Regulation of the Escherichia coli csgD promoter: interplay between five transcription factors., Microbiology 156(Pt 8):2470-83
[3] Prigent-Combaret C., Brombacher E., Vidal O., Ambert A., Lejeune P., Landini P., Dorel C., 2001, Complex regulatory network controls initial adhesion and biofilm formation in Escherichia coli via regulation of the csgD gene., J Bacteriol 183(24):7213-23
[4] Shimada T., Katayama Y., Kawakita S., Ogasawara H., Nakano M., Yamamoto K., Ishihama A., 2012, A novel regulator RcdA of the csgD gene encoding the master regulator of biofilm formation in Escherichia coli., Microbiologyopen 1(4):381-94
[5] Vianney A., Jubelin G., Renault S., Dorel C., Lejeune P., Lazzaroni JC., 2005, Escherichia coli tol and rcs genes participate in the complex network affecting curli synthesis., Microbiology 151(Pt 7):2487-97
[6] Ogasawara H., Yamamoto K., Ishihama A., 2011, Role of the biofilm master regulator CsgD in cross-regulation between biofilm formation and flagellar synthesis., J Bacteriol 193(10):2587-97
[7] 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
[8] Ogasawara H., Ishizuka T., Yamaji K., Kato Y., Shimada T., Ishihama A., 2019, Regulatory role of pyruvate-sensing BtsSR in biofilm formation by Escherichia coli K-12., FEMS Microbiol Lett 366(24)
[9] Reshamwala SM., Noronha SB., 2011, Biofilm formation in Escherichia coli cra mutants is impaired due to down-regulation of curli biosynthesis., Arch Microbiol 193(10):711-22
[10] 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
[11] Ogasawara H., Yamamoto K., Ishihama A., 2010, Regulatory role of MlrA in transcription activation of csgD, the master regulator of biofilm formation in Escherichia coli., FEMS Microbiol Lett 312(2):160-8
[12] Ogasawara H., Hasegawa A., Kanda E., Miki T., Yamamoto K., Ishihama A., 2007, Genomic SELEX search for target promoters under the control of the PhoQP-RstBA signal relay cascade., J Bacteriol 189(13):4791-9
[13] Ogasawara H., Shinohara S., Yamamoto K., Ishihama A., 2012, Novel regulation targets of the metal-response BasS-BasR two-component system of Escherichia coli., Microbiology 158(Pt 6):1482-92
[14] Azam MW., Zuberi A., Khan AU., 2020, bolA gene involved in curli amyloids and fimbriae production in E. coli: exploring pathways to inhibit biofilm and amyloid formation., J Biol Res (Thessalon) 27:10
[15] Soo VW., Wood TK., 2013, Antitoxin MqsA represses curli formation through the master biofilm regulator CsgD., Sci Rep 3:3186
[16] Pesavento C., Becker G., Sommerfeldt N., Possling A., Tschowri N., Mehlis A., Hengge R., 2008, Inverse regulatory coordination of motility and curli-mediated adhesion in Escherichia coli., Genes Dev 22(17):2434-46
[17] 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