RegulonDB

TRANSCRIPTION FACTOR:

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:

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	tcaaagcgtcATCGCATAAACCACTACATCttgctcctgt	[GEA]	[1] [2]
SoxS	activator	nfop	nfo	2250759	2250778	-37.0	caaagcgtcaTCGCATAAACCACTACATCTtgctcctgtt	[GEA]	[3] [2]
SoxS	activator	inaAp	inaA	2349531	2349550	-41.5	attcattaatACGACACGTTTCATTAAGATtttcctcagg	[GEA]	[2] [4] [5]
MarA	activator	tolCp4	tolC , ygiB , ygiC	3178012	3178031	-52.5	ttaacgccctATGGCACGTAACGCCAACCTtttgcggtag	[GEA]	[6] [7] [8]
MarA	activator	tolCp3	tolC , ygiB , ygiC	3178012	3178031	-40.5	ttaacgccctATGGCACGTAACGCCAACCTtttgcggtag	[AIBSCS] [GEA]	[6] [7] [8]
SoxS	activator	nfsBp	nfsB	605487	605506	-43.5	gcggaaatctATAGCGCATTTTTCTCGCTTaccatttctc	[GEA]	[9] [4]
MarA	activator	acrZp	acrZ	794701	794720	-40.5	cgcaaagctgACCGCACAAAAGGGGAGTGCttttctgtgc	[GEA]	[10]
Rob	activator	tolCp3	tolC , ygiB , ygiC	3178012	3178031	-40.5	ttaacgccctATGGCACGTAACGCCAACCTtttgcggtag	[AIBSCS] [GEA]	[6] [7] [8]
Rob	activator	nfsBp	nfsB	605487	605506	-43.5	gcggaaatctATAGCGCATTTTTCTCGCTTaccatttctc	[GEA]	[9]
Rob	activator	nfop	nfo	2250758	2250777	-38.5	tcaaagcgtcATCGCATAAACCACTACATCttgctcctgt	[GEA]	[11] [2]
Rob	activator	inaAp	inaA	2349531	2349550	-41.5	attcattaatACGACACGTTTCATTAAGATtttcctcagg	[GEA]	[12] [2] [13]
SoxS	activator	acrZp	acrZ	794701	794720	-40.5	cgcaaagctgACCGCACAAAAGGGGAGTGCttttctgtgc	[GEA]	[10]
Rob	activator	acrZp	acrZ	794701	794720	-40.5	cgcaaagctgACCGCACAAAAGGGGAGTGCttttctgtgc	[GEA]	[10]
MarA	activator	nfsBp	nfsB	605487	605506	-43.5	gcggaaatctATAGCGCATTTTTCTCGCTTaccatttctc	[GEA]	[14] [9]
SoxS	activator	tolCp3	tolC , ygiB , ygiC	3178012	3178031	-40.5	ttaacgccctATGGCACGTAACGCCAACCTtttgcggtag	[AIBSCS] [GEA]	[6] [7] [8]
MarA	activator	inaAp	inaA	2349531	2349550	-41.5	attcattaatACGACACGTTTCATTAAGATtttcctcagg	[GEA]	[2] [4] [5]
Rob	activator	tolCp4	tolC , ygiB , ygiC	3178012	3178031	-52.5	ttaacgccctATGGCACGTAACGCCAACCTtttgcggtag	[GEA]	[8]
SoxS	activator	tolCp4	tolC , ygiB , ygiC	3178012	3178031	-52.5	ttaacgccctATGGCACGTAACGCCAACCTtttgcggtag	[GEA]	[8]
SoxS	activator	nfop	nfo	2250770	2250789	-26.0	cgcataaaccACTACATCTTGCTCCTGTTAacccgctatc	[RSE]	[15]
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	actgaatgctAAAACAGCAAAAAATGCTATtatccaatta	[GEA]	[16]
MarA	repressor	robp	rob	4635363	4635382	-20.0	actgaatgctAAAACAGCAAAAAATGCTATtatccaatta	[GEA]	[16]
SoxS	repressor	robp	rob	4635363	4635382	-19.5	actgaatgctAAAACAGCAAAAAATGCTATtatccaatta		[16]

Evidence:

[GEA] Gene expression analysis
[AIBSCS] Automated inference based on similarity to consensus sequences
[RSE] RNA-seq evidence

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] Wang Z., et al., 2020
[14] Barbosa TM., et al., 2002
[15] Seo SW., et al., 2015
[16] 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] Wang Z., Xue T., Hu D., Ma Y., 2020, A Novel Butanol Tolerance-Promoting Function of the Transcription Factor Rob in Escherichia coli., Front Bioeng Biotechnol 8:524198
[14] 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
[15] 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
[16] Schneiders T., Levy SB., 2006, MarA-mediated transcriptional repression of the rob promoter., J Biol Chem 281(15):10049-55