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:

Rob	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Synonym(s):

CbpB, DNA-binding transcriptional dual regulator Rob, RobA, right origin-binding protein

Gene name(s):

rob

Functional conformation(s):

Rob

Coregulator(s):

AcrR, ArcA, CRP, CpxR, Cra, DnaA, EnvR, FNR, FadR, Fis, Fur, GadE-RcsB, H-NS, HU, IHF, Lrp, MarA, MarR, MprA, OmpR, OxyR, PhoP, Rob, SoxR, SoxS, ppGpp

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

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 , CpxR-phosphorylated

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 , 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:

SoxS	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Synonym(s):

DNA-binding transcriptional dual regulator SoxS, regulation of superoxide response regulon

Gene name(s):

soxS

Functional conformation(s):

SoxS

Coregulator(s):

AcrR, ArcA, BasR, CRP, CpxR, Cra, DnaA, EnvR, FNR, Fis, Fur, H-NS, HU, IHF, Lrp, MarA, MarR, Mlc, MprA, NarL, OmpR, OxyR, PhoP, Rob, SoxR, SoxS, Zur

Summary:

TF Summary ...[more]

TRANSCRIPTION FACTOR:

Info

Name:

MarA	Weight Matrix Tractordb tool

Connectivity class

Local Regulator

Synonym(s):

CfxB, DNA-binding transcriptional dual regulator MarA, InaR, NfxC, NorB, SoxQ

Gene name(s):

marA

Functional conformation(s):

MarA

Coregulator(s):

AcrR, ArcA, BasR, BluR, CRP, CpxR, Cra, DnaA, EnvR, FNR, Fis, FliZ, Fur, GadE, GadE-RcsB, GadW, GadX, H-NS, HU, IHF, LacI, Lrp, MarA, MarR, MprA, OmpR, OxyR, PhoP, PurR, PutA, RcsB, Rob, SoxR, SoxS, TorR, YdeO

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:

MarR	Tractordb tool

Connectivity class

Local Regulator

Synonym(s):

CfxB, DNA-binding transcriptional repressor MarR, InaR, SoxQ

Gene name(s):

marR

Functional conformation(s):

MarR-2,4-dinitrophenol , MarR-Benzoate , MarR-Menadione , MarR-Paraquat , MarR-Phenazine methosulfate , MarR-Plumbagin , MarR-Sodium salicylate , MarR , MarR-salicylate

Coregulator(s):

AcrR, CRP, CpxR, Cra, Fis, MarA, MarR, Rob, SoxS

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]

REGULATION EXERTED BY AcrR,CRP,CpxR,Cra,Fis,MarA,MarR,Rob,SoxS

Info M3D | Colombos

KNOWN BINDING SITES (The central relative position is relative to the promoter +1)
AcrR repressor CRP activator CpxR activator Cra repressor Fis activator MarA activator MarR repressor Rob activator SoxS activator
Transcription Factor		Regulated		Binding Sites				Evidence	References
Functional conformation	Function	Promoter	Gene(s)	LeftPos	RigthPos	Central Rel-Pos	Sequence
CRP-cyclic-AMP	activator	marRp	marR , marA , marB	1619030	1619051	-52.5	cgatttagcaAAACGTGGCATCGGTCAATTCAttcatttgac	[EXP-IEP-GENE-EXPRESSION-ANALYSIS] [EXP-IMP]	[1] [2]
Rob	activator	marRp	marR , marA , marB	1619022	1619041	-61.5	acttgaaccgATTTAGCAAAACGTGGCATCggtcaattca	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[3] [4] [5]
Fis	activator	marRp	marR , marA , marB	1619005	1619019	-81.0	gcatcgcattGAACAAAACTTGAACcgatttagca	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[5]
MarR	repressor	marRp	marR , marA , marB	1619098	1619119	17.0	cctgcaactaATTACTTGCCAGGGCAACTAATgtgaaaagta	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[6] [7] [8] [9] [10] [11]
MarR	repressor	marRp	marR , marA , marB	1619064	1619085	-18.0	catttgacttATACTTGCCTGGGCAATATTATcccctgcaac	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[6] [7] [8] [9] [10] [11]
Cra	repressor	marRp	marR , marA , marB	1619012	1619029	-72.5	attgaacaaaACTTGAACCGATTTAGCAaaacgtggca	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[12]
AcrR	repressor	marRp	marR , marA , marB	1619048	1619058	-40.5	catcggtcaaTTCATTCATTTgacttatact	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[13]
MarA	activator	marRp	marR , marA , marB	1619022	1619041	-61.5	acttgaaccgATTTAGCAAAACGTGGCATCggtcaattca	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[14] [15] [4] [16] [17]
SoxS	activator	marRp	marR , marA , marB	1619022	1619041	-61.5	acttgaaccgATTTAGCAAAACGTGGCATCggtcaattca	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[4] [16]
CpxR-phosphorylated	activator	marRp	marR , marA , marB	1619057	1619072	-29.0	attcattcatTTGACTTATACTTGCCtgggcaatat	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[18]

Evidence:

[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
[EXP-IMP] Inferred from mutant phenotype

Reference(s):

[1] Ruiz C., et al., 2010
[2] Zheng D., et al., 2004
[3] Bennik MH., et al., 2000
[4] Martin RG., et al., 1999
[5] Martin RG., et al., 1997
[6] Cohen SP., et al., 1993
[7] Martin RG., et al., 2004
[8] Martin RG., et al., 1995
[9] Notka F., et al., 2002
[10] Seoane AS., et al., 1995
[11] Shimada T., et al., 2018
[12] Shimada T., et al., 2011
[13] Lee JO., et al., 2014
[14] Belliveau NM., et al., 2018
[15] Gillette WK., et al., 2000
[16] Martin RG., et al., 1996
[17] Pomposiello PJ., et al., 2001
[18] Weatherspoon-Griffin N., et al., 2014

Reference(s)
[1] Ruiz C., Levy SB., 2010, Many chromosomal genes modulate MarA-mediated multidrug resistance in Escherichia coli., Antimicrob Agents Chemother 54(5):2125-34
[2] 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
[3] Bennik MH., Pomposiello PJ., Thorne DF., Demple B., 2000, Defining a rob regulon in Escherichia coli by using transposon mutagenesis., J Bacteriol 182(13):3794-801
[4] Martin RG., Gillette WK., Rhee S., Rosner JL., 1999, Structural requirements for marbox function in transcriptional activation of mar/sox/rob regulon promoters in Escherichia coli: sequence, orientation and spatial relationship to the core promoter., Mol Microbiol 34(3):431-41
[5] Martin RG., Rosner JL., 1997, Fis, an accessorial factor for transcriptional activation of the mar (multiple antibiotic resistance) promoter of Escherichia coli in the presence of the activator MarA, SoxS, or Rob., J Bacteriol 179(23):7410-9
[6] Cohen SP., Hachler H., Levy SB., 1993, Genetic and functional analysis of the multiple antibiotic resistance (mar) locus in Escherichia coli., J Bacteriol 175(5):1484-92
[7] Martin RG., Rosner JL., 2004, Transcriptional and translational regulation of the marRAB multiple antibiotic resistance operon in Escherichia coli., Mol Microbiol 53(1):183-91
[8] Martin RG., Rosner JL., 1995, Binding of purified multiple antibiotic-resistance repressor protein (MarR) to mar operator sequences., Proc Natl Acad Sci U S A 92(12):5456-60
[9] Notka F., Linde HJ., Dankesreiter A., Niller HH., Lehn N., 2002, A C-terminal 18 amino acid deletion in MarR in a clinical isolate of Escherichia coli reduces MarR binding properties and increases the MIC of ciprofloxacin., J Antimicrob Chemother 49(1):41-7
[10] Seoane AS., Levy SB., 1995, Characterization of MarR, the repressor of the multiple antibiotic resistance (mar) operon in Escherichia coli., J Bacteriol 177(12):3414-9
[11] Shimada T., Ogasawara H., Ishihama A., 2018, Single-target regulators form a minor group of transcription factors in Escherichia coli K-12., Nucleic Acids Res 46(8):3921-3936
[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] Lee JO., Cho KS., Kim OB., 2014, Overproduction of AcrR increases organic solvent tolerance mediated by modulation of SoxS regulon in Escherichia coli., Appl Microbiol Biotechnol 98(20):8763-73
[14] Belliveau NM., Barnes SL., Ireland WT., Jones DL., Sweredoski MJ., Moradian A., Hess S., Kinney JB., Phillips R., 2018, Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria., Proc Natl Acad Sci U S A 115(21):E4796-E4805
[15] Gillette WK., Martin RG., Rosner JL., 2000, Probing the Escherichia coli transcriptional activator MarA using alanine-scanning mutagenesis: residues important for DNA binding and activation., J Mol Biol 299(5):1245-55
[16] Martin RG., Jair KW., Wolf RE., Rosner JL., 1996, Autoactivation of the marRAB multiple antibiotic resistance operon by the MarA transcriptional activator in Escherichia coli., J Bacteriol 178(8):2216-23
[17] Pomposiello PJ., Bennik MH., Demple B., 2001, Genome-wide transcriptional profiling of the Escherichia coli responses to superoxide stress and sodium salicylate., J Bacteriol 183(13):3890-902
[18] Weatherspoon-Griffin N., Yang D., Kong W., Hua Z., Shi Y., 2014, The CpxR/CpxA two-component regulatory system up-regulates the multidrug resistance cascade to facilitate Escherichia coli resistance to a model antimicrobial peptide., J Biol Chem 289(47):32571-82