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MarA,Rob,SoxS regulon in Escherichia coli K-12 genome


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-RcsB, H-NS, HU, IHF, Lrp, MarA, MarR, MprA, OmpR, OxyR, PhoP, Rob, SoxR, SoxS
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]

REGULATION EXERTED BY MarA,Rob,SoxS Info M3D | Colombos
KNOWN BINDING SITES (The central relative position is relative to the promoter +1)    
MarA activator Rob activator SoxS activator    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
MarA activator nfop nfo 2250758 2250777 -38.5 tcaaagcgtcATCGCATAAACCACTACATCTtgctcctgtt   [1]
[2]
SoxS activator nfop nfo 2250759 2250778 -37.0 caaagcgtcaTCGCATAAACCACTACATCTTgctcctgtta   [3]
[2]
SoxS activator inaAp inaA 2349531 2349550 -41.5 aattcattaaTACGACACGTTTCATTAAGATtttcctcagg   [2]
[4]
[5]
MarA activator tolCp4 tolC , ygiB , ygiC 3178012 3178032 -52.5 ttaacgccctATGGCACGTAACGCCAACCTTttgcggtagc   [6]
[7]
[8]
MarA activator tolCp3 tolC , ygiB , ygiC 3178012 3178032 -40.5 ttaacgccctATGGCACGTAACGCCAACCTTttgcggtagc [AIBSCS]
[GEA]
[6]
[7]
[8]
SoxS activator nfsBp nfsB 605487 605507 -43.5 agcggaaatcTATAGCGCATTTTTCTCGCTTaccatttctc   [9]
[4]
MarA activator acrZp acrZ 794701 794720 -40.5 cgcaaagctgACCGCACAAAAGGGGAGTGCTtttctgtgct   [10]
Rob activator tolCp3 tolC , ygiB , ygiC 3178012 3178032 -40.5 ttaacgccctATGGCACGTAACGCCAACCTTttgcggtagc [AIBSCS]
[GEA]
[6]
[7]
[8]
Rob activator nfsBp nfsB 605487 605507 -43.5 agcggaaatcTATAGCGCATTTTTCTCGCTTaccatttctc   [9]
Rob activator nfop nfo 2250758 2250777 -38.5 tcaaagcgtcATCGCATAAACCACTACATCTtgctcctgtt   [11]
[2]
Rob activator inaAp inaA 2349531 2349550 -41.5 aattcattaaTACGACACGTTTCATTAAGATtttcctcagg   [12]
[2]
SoxS activator acrZp acrZ 794701 794720 -40.5 cgcaaagctgACCGCACAAAAGGGGAGTGCTtttctgtgct   [10]
Rob activator acrZp acrZ 794701 794720 -40.5 cgcaaagctgACCGCACAAAAGGGGAGTGCTtttctgtgct   [10]
MarA activator nfsBp nfsB 605487 605507 -43.5 agcggaaatcTATAGCGCATTTTTCTCGCTTaccatttctc   [13]
[9]
SoxS activator tolCp3 tolC , ygiB , ygiC 3178012 3178032 -40.5 ttaacgccctATGGCACGTAACGCCAACCTTttgcggtagc [AIBSCS]
[GEA]
[6]
[7]
[8]
MarA activator inaAp inaA 2349531 2349550 -41.5 aattcattaaTACGACACGTTTCATTAAGATtttcctcagg   [2]
[4]
[5]
Rob activator tolCp4 tolC , ygiB , ygiC 3178012 3178032 -52.5 ttaacgccctATGGCACGTAACGCCAACCTTttgcggtagc   [8]
SoxS activator tolCp4 tolC , ygiB , ygiC 3178012 3178032 -52.5 ttaacgccctATGGCACGTAACGCCAACCTTttgcggtagc   [8]
SoxS activator nfop nfo 2250770 2250789 -26.0 cgcataaaccACTACATCTTGCTCCTGTTAAcccgctatca   [14]
MarA repressor Rob repressor SoxS repressor    
Transcription Factor
Regulated
Binding Sites
Evidence
References
Functional conformation
Function
Promoter
Gene(s)
LeftPos
RigthPos
Central Rel-Pos
Sequence
Rob repressor robp rob 4635363 4635382 -19.5 cactgaatgcTAAAACAGCAAAAAATGCTATtatccaatta   [15]
MarA repressor robp rob 4635363 4635382 -20.0 cactgaatgcTAAAACAGCAAAAAATGCTATtatccaatta   [15]
SoxS repressor robp rob 4635363 4635382 -19.5 cactgaatgcTAAAACAGCAAAAAATGCTATtatccaatta   [15]

Evidence: [AIBSCS] Automated inference based on similarity to consensus sequences
[GEA] Gene expression analysis
Reference(s): [1] Jair KW., et al., 1995
[2] Martin RG., et al., 1999
[3] Jair KW., et al., 1996
[4] Martin RG., et al., 2011
[5] Pomposiello PJ., et al., 2001
[6] Aono R., et al., 1998
[7] Rodionov DA., et al., 2001
[8] Zhang A., et al., 2008
[9] Martin RG., et al., 2002
[10] Hobbs EC., et al., 2012
[11] Ariza RR., et al., 1995
[12] Bennik MH., et al., 2000
[13] Barbosa TM., et al., 2002
[14] Seo SW., et al., 2015
[15] Schneiders T., et al., 2006



Reference(s)    

 [1] Jair KW., Martin RG., Rosner JL., Fujita N., Ishihama A., Wolf RE., 1995, Purification and regulatory properties of MarA protein, a transcriptional activator of Escherichia coli multiple antibiotic and superoxide resistance promoters., J Bacteriol 177(24):7100-4

 [2] 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

 [3] Jair KW., Fawcett WP., Fujita N., Ishihama A., Wolf RE., 1996, Ambidextrous transcriptional activation by SoxS: requirement for the C-terminal domain of the RNA polymerase alpha subunit in a subset of Escherichia coli superoxide-inducible genes., Mol Microbiol 19(2):307-17

 [4] 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

 [5] 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

 [6] Aono R., Tsukagoshi N., Yamamoto M., 1998, Involvement of outer membrane protein TolC, a possible member of the mar-sox regulon, in maintenance and improvement of organic solvent tolerance of Escherichia coli K-12., J Bacteriol 180(4):938-44

 [7] 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

 [8] Zhang A., Rosner JL., Martin RG., 2008, Transcriptional activation by MarA, SoxS and Rob of two tolC promoters using one binding site: a complex promoter configuration for tolC in Escherichia coli., Mol Microbiol 69(6):1450-5

 [9] Martin RG., Rosner JL., 2002, Genomics of the marA/soxS/rob regulon of Escherichia coli: identification of directly activated promoters by application of molecular genetics and informatics to microarray data., Mol Microbiol 44(6):1611-24

 [10] Hobbs EC., Yin X., Paul BJ., Astarita JL., Storz G., 2012, Conserved small protein associates with the multidrug efflux pump AcrB and differentially affects antibiotic resistance., Proc Natl Acad Sci U S A 109(41):16696-701

 [11] Ariza RR., Li Z., Ringstad N., Demple B., 1995, Activation of multiple antibiotic resistance and binding of stress-inducible promoters by Escherichia coli Rob protein., J Bacteriol 177(7):1655-61

 [12] 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

 [13] Barbosa TM., Levy SB., 2002, Activation of the Escherichia coli nfnB gene by MarA through a highly divergent marbox in a class II promoter., Mol Microbiol 45(1):191-202

 [14] Seo SW., Kim D., Szubin R., Palsson BO., 2015, Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655., Cell Rep 12(8):1289-99

 [15] Schneiders T., Levy SB., 2006, MarA-mediated transcriptional repression of the rob promoter., J Biol Chem 281(15):10049-55


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