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Rob DNA-binding transcriptional dual regulator

Synonyms: Rob
Summary:
Rob is a transcriptional dual regulator. Its N-terminal domain shares 49% identity with MarA and SoxS [15] These proteins activate a common set of about 50 target genes [1, 16, 17, 18] the marA/soxS/rob regulon, involved in antibiotic resistance [10, 19, 20] superoxide resistance [5, 21, 22] and tolerance to organic solvents [23, 24]and heavy metals [25] The activity of each protein is induced by different signals: the activity of Rob is increased with dipyridyl, bile salts, or decanoate [2, 26] and the activities of MarA and SoxS are increased by the aromatic weak acid salicylate [18]and oxidative stress [27] respectively.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
Rob     nd nd
Evolutionary Family: AraC/XylS
Connectivity class: Local Regulator
Gene name: rob
  Genome position: 4634441-4635310
  Length: 870 bp / 289 aa
Operon name: rob
TU(s) encoding the TF:
Transcription unit        Promoter
rob
robp


Regulon       
Regulated gene(s) acnA, acrA, acrB, acrZ, aslB, fumC, inaA, ldtB, marA, marB, marR, micF, mltF, nfo, nfsA, nfsB, rimK, rob, sodA, tolC, ybjC, ybjN, ygiA, ygiB, ygiC, zwf
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
drug resistance/sensitivity (7)
adaptations (3)
Transcription related (3)
detoxification (3)
TCA cycle (2)
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Regulated operon(s) acnA, acrAB, acrZ, aslB, fumAC, inaA, ldtB, marRAB, micF, mltF, nfo, nfsB, rob, sodA, tolC-ygiABC, ybjC-nfsA-rimK-ybjN, zwf
First gene in the operon(s) acnA, acrA, acrZ, aslB, fumC, inaA, ldtB, marR, micF, mltF, nfo, nfsB, rob, sodA, tolC, tolC, ybjC, zwf
Simple and complex regulons AcrR,CRP,CpxR,Cra,Fis,MarA,MarR,Rob,SoxS
AcrR,EnvR,MarA,MprA,PhoP,Rob,SoxS
AcrR,H-NS,HU,IHF,Lrp,MarA,OmpR,Rob,SoxS
ArcA,CRP,Cra,FNR,MarA,Rob,SoxS
ArcA,CRP,FNR,Fur,IHF,MarA,Rob,SoxS
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Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[Rob,-](1)
[Rob,+](13)


Transcription factor binding sites (TFBSs) arrangements       

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence
LeftPos RightPos Growth Conditions Evidence (Confirmed, Strong, Weak) References
  Rob activator acnAp2 Sigma70 -51.5 -101.5 acnA
aaggtttctcCTCTTTTATCAATTTGGGTTgttatcaaat
1335720 1335739 nd [GEA], [HIBSCS] [1]
  Rob activator acrAp Sigma70 nd nd acrA, acrB nd nd [a] [BPP], [GEA] [2]
  Rob activator acrZp Sigma70 -40.5 -62.5 acrZ
cgcaaagctgACCGCACAAAAGGGGAGTGCttttctgtgc
794701 794720 nd [GEA], [IHBCE] [3]
  Rob activator aslBp Sigma54 nd nd aslB nd nd nd [GEA] [4]
  Rob activator fumCp1 Sigma70 -35.5 -101.5 fumC
gtttttttacATGGCACGAAAGACCAAACAtttgttatca
1686680 1686699 nd [BPP], [GEA], [IEP] [5], [6]
  Rob activator inaAp Sigma70 -41.5 -68.5 inaA
attcattaatACGACACGTTTCATTAAGATtttcctcagg
2349531 2349550 [a] [BPP], [GEA], [HIBSCS] [4], [7]
  Rob activator marRp Sigma70 -61.5 -88.5 marR, marA, marB
acttgaaccgATTTAGCAAAACGTGGCATCggtcaattca
1619022 1619041 nd [BPP], [GEA], [HIBSCS], [SM] [4], [7], [8]
  Rob activator micFp Sigma70 -40.0 -40.5 micF
aagtatttgaCAGCACTGAATGTCAAAACAaaaccttcac
2313034 2313053 nd [BPP], [GEA], [HIBSCS] [9]
  Rob activator mltFp Sigma70 nd nd mltF nd nd nd [GEA] [4]
  Rob activator nfop Sigma70 -38.5 -72.5 nfo
tcaaagcgtcATCGCATAAACCACTACATCttgctcctgt
2250758 2250777 nd [GEA], [HIBSCS] [7], [10]
  Rob activator nfsBp Sigma70 -43.5 -72.5 nfsB
gcggaaatctATAGCGCATTTTTCTCGCTTaccatttctc
605487 605506 nd [GEA], [HIBSCS] [1]
  Rob repressor robp nd -19.5 -62.5 rob
actgaatgctAAAACAGCAAAAAATGCTATtatccaatta
4635363 4635382 nd [BPP], [GEA], [HIBSCS] [11]
  Rob activator sodAp Sigma70 -40.5 -91.5 sodA
tacgaaaagtACGGCATTGATAATCATTTTcaatatcatt
4100709 4100728 nd [HIBSCS] [10]
  Rob activator tolCp3 nd -40.5 -93.5 tolC, ygiA, ygiB, ygiC
ttaacgccctATGGCACGTAACGCCAACCTtttgcggtag
3178012 3178031 nd [AIBSCS], [GEA] [12], [13], [14]
  Rob activator tolCp4 Sigma38 -52.5 -93.5 tolC, ygiA, ygiB, ygiC
ttaacgccctATGGCACGTAACGCCAACCTtttgcggtag
3178012 3178031 nd [AIBSCS], [GEA] [12], [13], [14]
  Rob activator ybisp nd nd nd ldtB nd nd nd [GEA] [4]
  Rob activator ybjCp Sigma70 -40.5 -61.5 ybjC, nfsA, rimK, ybjN
ttaattgctaAAAGCTATAACTGTTAAACAcaatacagtg
890842 890861 nd [GEA], [HIBSCS] [1]
  Rob activator zwfp Sigma70 -54.0 -115.5 zwf
gcttttcccgTAATCGCACGGGTGGATAAGcgtttacagt
1936420 1936439 nd [BPP] [5], [10]


Growth Condition    

 [a] Bile salts treatment



Alignment and PSSM for Rob TFBSs    

Position weight matrix (PWM).   
A	13	1	4	2	0	11	3	4	6	9	6	1	5	3	1	13	9
C	0	6	3	1	12	1	8	0	1	0	2	3	0	5	4	0	1
G	0	0	6	10	0	0	0	6	3	2	0	4	8	1	1	0	1
T	0	6	0	0	1	1	2	3	3	2	5	5	0	4	7	0	2

PWM logo   


 


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
TF-target gene evolutionary conservation
Promoter-target gene evolutionary conservation


Evidence    

 [GEA] Gene expression analysis

 [HIBSCS] Human inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins

 [IHBCE] Inferred by a human based on computational evidence

 [IEP] Inferred from expression pattern

 [SM] Site mutation

 [AIBSCS] Automated inference based on similarity to consensus sequences



Reference(s)    

 [1] 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

 [2] Rosenberg EY., Bertenthal D., Nilles ML., Bertrand KP., Nikaido H., 2003, Bile salts and fatty acids induce the expression of Escherichia coli AcrAB multidrug efflux pump through their interaction with Rob regulatory protein., Mol Microbiol. 48(6):1609-19

 [3] 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

 [4] 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

 [5] Jair KW., Yu X., Skarstad K., Thony B., Fujita N., Ishihama A., Wolf RE., 1996, Transcriptional activation of promoters of the superoxide and multiple antibiotic resistance regulons by Rob, a binding protein of the Escherichia coli origin of chromosomal replication., J Bacteriol. 178(9):2507-13

 [6] Taliaferro LP., Keen EF., Sanchez-Alberola N., Wolf RE., 2012, Transcription Activation by Escherichia coli Rob at Class II Promoters: Protein-Protein Interactions between Rob's N-Terminal Domain and the ¿¿(70) Subunit of RNA Polymerase., J Mol Biol. 419(3-4):139-57

 [7] 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

 [8] 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

 [9] Kwon HJ., Bennik MH., Demple B., Ellenberger T., 2000, Crystal structure of the Escherichia coli Rob transcription factor in complex with DNA., Nat Struct Biol. 7(5):424-30

 [10] 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

 [11] Schneiders T., Levy SB., 2006, MarA mediated transcriptional repression of the rob promoter., J Biol Chem. 281(15):10049-51

 [12] 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

 [13] 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

 [14] 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

 [15] 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

 [16] Barbosa TM., Levy SB., 2000, Differential expression of over 60 chromosomal genes in Escherichia coli by constitutive expression of MarA., J Bacteriol. 182(12):3467-74

 [17] Martin RG., Rosner JL., 2003, Analysis of microarray data for the marA, soxS, and rob regulons of Escherichia coli., Methods Enzymol. 370:278-80

 [18] 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

 [19] 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

 [20] Griffith KL., Becker SM., Wolf RE., 2005, Characterization of TetD as a transcriptional activator of a subset of genes of the Escherichia coli SoxS/MarA/Rob regulon., Mol Microbiol. 56(4):1103-17

 [21] Nunoshiba T., Hidalgo E., Amabile Cuevas CF., Demple B., 1992, Two-stage control of an oxidative stress regulon: the Escherichia coli SoxR protein triggers redox-inducible expression of the soxS regulatory gene., J Bacteriol. 174(19):6054-60

 [22] Wu J., Weiss B., 1992, Two-stage induction of the soxRS (superoxide response) regulon of Escherichia coli., J Bacteriol. 174(12):3915-20

 [23] White DG., Goldman JD., Demple B., Levy SB., 1997, Role of the acrAB locus in organic solvent tolerance mediated by expression of marA, soxS, or robA in Escherichia coli., J Bacteriol. 179(19):6122-6

 [24] Aono R., 1998, Improvement of organic solvent tolerance level of Escherichia coli by overexpression of stress-responsive genes., Extremophiles. 2(3):239-48

 [25] Nakajima H., Kobayashi K., Kobayashi M., Asako H., Aono R., 1995, Overexpression of the robA gene increases organic solvent tolerance and multiple antibiotic and heavy metal ion resistance in Escherichia coli., Appl Environ Microbiol. 61(6):2302-7

 [26] Rosner JL., Dangi B., Gronenborn AM., Martin RG., 2002, Posttranscriptional activation of the transcriptional activator Rob by dipyridyl in Escherichia coli., J Bacteriol. 184(5):1407-16

 [27] Demple B., 1996, Redox signaling and gene control in the Escherichia coli soxRS oxidative stress regulon--a review., Gene. 179(1):53-7

 [28] Chubiz LM., Glekas GD., Rao CV., 2012, Transcriptional cross talk within the mar-sox-rob regulon in Escherichia coli is limited to the rob and marRAB operons., J Bacteriol. 194(18):4867-75

 [29] Pomposiello PJ., Koutsolioutsou A., Carrasco D., Demple B., 2003, SoxRS-regulated expression and genetic analysis of the yggX gene of Escherichia coli., J Bacteriol. 185(22):6624-32

 [30] Wood TI., Griffith KL., Fawcett WP., Jair KW., Schneider TD., Wolf RE., 1999, Interdependence of the position and orientation of SoxS binding sites in the transcriptional activation of the class I subset of Escherichia coli superoxide-inducible promoters., Mol Microbiol. 34(3):414-30

 [31] Dangi B., Pelupessey P., Martin RG., Rosner JL., Louis JM., Gronenborn AM., 2001, Structure and dynamics of MarA-DNA complexes: an NMR investigation., J Mol Biol. 314(1):113-27

 [32] Griffith KL., Wolf RE., 2001, Systematic mutagenesis of the DNA binding sites for SoxS in the Escherichia coli zwf and fpr promoters: identifying nucleotides required for DNA binding and transcription activation., Mol Microbiol. 40(5):1141-54

 [33] Griffith KL., Shah IM., Myers TE., O'Neill MC., Wolf RE., 2002, Evidence for pre-recruitment as a new mechanism of transcription activation in Escherichia coli: the large excess of SoxS binding sites per cell relative to the number of SoxS molecules per cell., Biochem Biophys Res Commun. 291(4):979-86

 [34] Martin RG., Gillette WK., Martin NI., Rosner JL., 2002, Complex formation between activator and RNA polymerase as the basis for transcriptional activation by MarA and SoxS in Escherichia coli., Mol Microbiol. 43(2):355-70

 [35] Gallegos MT., Schleif R., Bairoch A., Hofmann K., Ramos JL., 1997, Arac/XylS family of transcriptional regulators., Microbiol Mol Biol Rev. 61(4):393-410

 [36] Griffith KL., Wolf RE., 2002, A comprehensive alanine scanning mutagenesis of the Escherichia coli transcriptional activator SoxS: identifying amino acids important for DNA binding and transcription activation., J Mol Biol. 322(2):237-57

 [37] Rhee S., Martin RG., Rosner JL., Davies DR., 1998, A novel DNA-binding motif in MarA: the first structure for an AraC family transcriptional activator., Proc Natl Acad Sci U S A. 95(18):10413-8

 [38] Rodgers ME., Schleif R., 2009, Solution structure of the DNA binding domain of AraC protein., Proteins. 77(1):202-8

 [39] Griffith KL., Fitzpatrick MM., Keen EF., Wolf RE., 2009, Two functions of the C-terminal domain of Escherichia coli Rob: mediating sequestration-dispersal as a novel off-on switch for regulating Rob's activity as a transcription activator and preventing degradation of Rob by Lon protease., J Mol Biol. 388(3):415-30

 [40] Skarstad K., Thony B., Hwang DS., Kornberg A., 1993, A novel binding protein of the origin of the Escherichia coli chromosome., J Biol Chem. 268(8):5365-70

 [41] Ali Azam T., Iwata A., Nishimura A., Ueda S., Ishihama A., 1999, Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid., J Bacteriol. 181(20):6361-70

 [42] Kakeda M., Ueguchi C., Yamada H., Mizuno T., 1995, An Escherichia coli curved DNA-binding protein whose expression is affected by the stationary phase-specific sigma factor sigma S., Mol Gen Genet. 248(5):629-34

 [43] Alekshun MN., Levy SB., 1999, The mar regulon: multiple resistance to antibiotics and other toxic chemicals., Trends Microbiol. 7(10):410-3

 [44] Randall LP., Woodward MJ., 2002, The multiple antibiotic resistance (mar) locus and its significance., Res Vet Sci. 72(2):87-93



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