RegulonDB RegulonDB 10.6.3: Regulon Form
   
   


AcrR,CRP,CpxR,Cra,Fis,MarA,MarR,Rob,SoxS regulon in Escherichia coli K-12 genome


TRANSCRIPTION FACTOR: Info
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, GadW, GadX, GlcC, GlpR, H-NS, HprR, IHF, IscR, LeuO, Lrp, MalT, MarA, MarR, MazE, Mlc, MntR, ModE, NanR, NarL, NarP, NrdR, NsrR, NtrC, OmpR, OxyR, PdhR, PepA, PurR, RcsB, 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, Fis, Fur, GadE, H-NS, HU, IHF, Lrp, MarA, MarR, MprA, OmpR, OxyR, PhoP, Rob, SoxR, SoxS
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-Phosphorylated , CpxR
Coregulator(s): AcrR, BaeR, BasR, CRP, CpxR, Cra, CsgD, CysB, EnvY, Fis, FliZ, Fur, GadE, H-NS, IHF, Lrp, MarA, MarR, MlrA, MqsA, NsrR, OmpR, PdhR, PhoB, RcdA, 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-cAMP , CRP
Coregulator(s): AcrR, AdiY, AgaR, AraC, ArcA, ArgP, ArgR, AscG, BasR, BtsR, CRP, 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, FucR, Fur, GadE, 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, PrpR, PurR, PuuR, QseB, RbsR, RcdA, RcsB, RhaR, RhaS, Rob, RstA, SdiA, SlyA, SoxR, SoxS, SrlR, StpA, TdcA, TdcR, TorR, TreR, UhpA, UidR, UlaR, UvrY, UxuR, XylR, YdeO, YiaJ, 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, 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, CRP, CpxR, Cra, DnaA, EnvR, FNR, Fis, FliZ, Fur, GadE, GadW, GadX, H-NS, HU, IHF, 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 , Cra-β-D-fructofuranose 1-phosphate , Cra-β-D-fructose 1,6-bisphosphate
Coregulator(s): AcrR, ArcA, BasR, BetI, CRP, CpxR, Cra, CsgD, CusR, 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, RcsB, 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 , MarR-salicylate , MarR-2,4-dinitrophenol , MarR-Benzoate , MarR-Menadione , MarR-Paraquat , MarR-Phenazine methosulfate , MarR-Plumbagin , MarR-Sodium 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-ethidium , AcrR , AcrR-Proflavin , AcrR-R6G
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, RcsB, 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-cAMP activator marRp marR , marA , marB 1619030 1619051 -52.5 cgatttagcaAAACGTGGCATCGGTCAATTCAttcatttgac [AIBSCS]
[GEA]
[IMP]
[1]
[2]
Rob activator marRp marR , marA , marB 1619022 1619041 -61.5 acttgaaccgATTTAGCAAAACGTGGCATCggtcaattca [BPP]
[GEA]
[HIBSCS]
[SM]
[3]
[4]
[5]
Fis activator marRp marR , marA , marB 1619005 1619019 -81.0 gcatcgcattGAACAAAACTTGAACcgatttagca [BPP]
[GEA]
[SM]
[5]
MarR repressor marRp marR , marA , marB 1619098 1619119 17.0 cctgcaactaATTACTTGCCAGGGCAACTAATgtgaaaagta [AIBSCS]
[BPP]
[GEA]
[GS]
[HIBSCS]
[SM]
[6]
[7]
[8]
[9]
[10]
[11]
[12]
MarR repressor marRp marR , marA , marB 1619064 1619085 -18.0 catttgacttATACTTGCCTGGGCAATATTATcccctgcaac [AIBSCS]
[BPP]
[GEA]
[GS]
[HIBSCS]
[SM]
[6]
[7]
[8]
[9]
[10]
[11]
[12]
Cra repressor marRp marR , marA , marB 1619012 1619029 -72.5 attgaacaaaACTTGAACCGATTTAGCAaaacgtggca [AIBSCS]
[GEA]
[13]
AcrR repressor marRp marR , marA , marB 1619048 1619058 -40.5 catcggtcaaTTCATTCATTTgacttatact [BPP]
[GEA]
[HIBSCS]
[14]
CpxR-Phosphorylated activator marRp marR , marA , marB 1619057 1619072 -29.0 attcattcatTTGACTTATACTTGCCtgggcaatat [BPP]
[GEA]
[HIBSCS]
[15]
MarA activator marRp marR , marA , marB 1619022 1619041 -61.5 acttgaaccgATTTAGCAAAACGTGGCATCggtcaattca [AIBSCS]
[BPP]
[GEA]
[HIBSCS]
[SM]
[16]
[17]
[4]
[18]
[19]
[20]
[10]
SoxS activator marRp marR , marA , marB 1619022 1619041 -61.5 acttgaaccgATTTAGCAAAACGTGGCATCggtcaattca [BPP]
[GEA]
[HIBSCS]
[4]
[18]
[19]

Evidence: [AIBSCS] Automated inference based on similarity to consensus sequences
[GEA] Gene expression analysis
[IMP] Inferred from mutant phenotype
[BPP] Binding of purified proteins
[HIBSCS] Human inference based on similarity to consensus sequences
[SM] Site mutation
[GS] genomic SELEX
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] Rodionov DA., et al., 2001
[11] Seoane AS., et al., 1995
[12] Shimada T., et al., 2018
[13] Shimada T., et al., 2011
[14] Lee JO., et al., 2014
[15] Weatherspoon-Griffin N., et al., 2014
[16] Belliveau NM., et al., 2018
[17] Gillette WK., et al., 2000
[18] Martin RG., et al., 1996
[19] Martin RG., et al., 2011
[20] Pomposiello PJ., et al., 2001



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] Rodionov DA., Gelfand MS., Mironov AA., Rakhmaninova AB., 2001, Comparative approach to analysis of regulation in complete genomes: multidrug resistance systems in gamma-proteobacteria., J Mol Microbiol Biotechnol 3(2):319-24

 [11] 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

 [12] 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

 [13] 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

 [14] 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

 [15] 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

 [16] 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

 [17] 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

 [18] 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

 [19] Martin RG., Rosner JL., 2011, Promoter discrimination at class I MarA regulon promoters mediated by glutamic acid 89 of the MarA transcriptional activator of Escherichia coli., J Bacteriol 193(2):506-15

 [20] 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


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