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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 |CITS:[8383113]|. These proteins activate a common set of about 50 target genes |CITS:[10852879][12067348][14712652][11395452]|, the marA/soxS/rob regulon, involved in antibiotic resistance |CITS:[8636021][15853893][7896685]|, superoxide resistance |CITS:[8626315][1400156][1317841]|, and tolerance to organic solvents |CITS:[9324261][9783171]| and heavy metals |CITS:[7793951]|. The activity of each protein is induced by different signals: the activity of Rob is increased with dipyridyl, bile salts, or decanoate |CITS:[11844771][12791142]|, and the activities of MarA and SoxS are increased by the aromatic weak acid salicylate |CITS:[11395452]| and oxidative stress |CITS:[8955629]|, respectively. Cross talk between the mar and rob systems plays an important role in the response to salicylate |CITS:[22753060]|.
Many genes are regulated by all three proteins; however, some genes are regulated by only one of them. The differential regulation of these genes might be caused by the degeneracy of their DNA-binding sites |CITS:[14594836]|.
Rob, MarA, and SoxS bind as monomers to the same DNA site, a degenerate 20-bp sequence known as the Mar-Sox-Rob box, which has to be in a specific orientation and distance relative to the -35 and -10 boxes of the promoter |CITS:[10564485][10564484]|. In class I promoters, the activators bind upstream of the -35 box and are generally oriented in the backward direction, while in class II promoters the proteins overlap the -35 promoter hexamer and generally are oriented in the forward direction |CITS:[10564485][10564484][22465792]|.
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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 Evidence (Confirmed, Strong, Weak) References
  Rob activator acnAp2 Sigma70 -51.5 -101.5 acnA
aaggtttctcCTCTTTTATCAATTTGGGTTgttatcaaat
1335720 1335739 [GEA], [HIBSCS] [1]
  Rob activator acrAp Sigma70 nd nd acrA, acrB nd nd [BPP], [GEA] [2]
  Rob activator acrZp Sigma70 -40.5 -62.5 acrZ
cgcaaagctgACCGCACAAAAGGGGAGTGCttttctgtgc
794701 794720 [GEA], [IHBCE] [3]
  Rob activator aslBp Sigma54 nd nd aslB nd nd [GEA] [4]
  Rob activator fumCp1 Sigma70 -35.5 -101.5 fumC
gtttttttacATGGCACGAAAGACCAAACAtttgttatca
1686680 1686699 [BPP], [GEA], [IEP] [5], [6]
  Rob activator inaAp Sigma70 -41.5 -68.5 inaA
attcattaatACGACACGTTTCATTAAGATtttcctcagg
2349531 2349550 [BPP], [GEA], [HIBSCS] [4], [7]
  Rob activator marRp Sigma70 -61.5 -88.5 marR, marA, marB
acttgaaccgATTTAGCAAAACGTGGCATCggtcaattca
1619022 1619041 [BPP], [GEA], [HIBSCS], [SM] [4], [7], [8]
  Rob activator micFp Sigma70 -40.0 -40.5 micF
aagtatttgaCAGCACTGAATGTCAAAACAaaaccttcac
2313034 2313053 [BPP], [GEA], [HIBSCS] [9]
  Rob activator mltFp Sigma70 nd nd mltF nd nd [GEA] [4]
  Rob activator nfop Sigma70 -38.5 -72.5 nfo
tcaaagcgtcATCGCATAAACCACTACATCttgctcctgt
2250758 2250777 [GEA], [HIBSCS] [7], [10]
  Rob activator nfsBp Sigma70 -43.5 -72.5 nfsB
gcggaaatctATAGCGCATTTTTCTCGCTTaccatttctc
605487 605506 [GEA], [HIBSCS] [1]
  Rob repressor robp nd -19.5 -62.5 rob
actgaatgctAAAACAGCAAAAAATGCTATtatccaatta
4635363 4635382 [BPP], [GEA], [HIBSCS] [11]
  Rob activator sodAp Sigma70 -40.5 -91.5 sodA
tacgaaaagtACGGCATTGATAATCATTTTcaatatcatt
4100709 4100728 [HIBSCS] [10]
  Rob activator tolCp3 nd -40.5 -93.5 tolC, ygiA, ygiB, ygiC
ttaacgccctATGGCACGTAACGCCAACCTtttgcggtag
3178012 3178031 [AIBSCS], [GEA] [12], [13], [14]
  Rob activator tolCp4 Sigma38 -52.5 -93.5 tolC, ygiA, ygiB, ygiC
ttaacgccctATGGCACGTAACGCCAACCTtttgcggtag
3178012 3178031 [AIBSCS], [GEA] [12], [13], [14]
  Rob activator ybisp nd nd nd ldtB nd nd [GEA] [4]
  Rob activator ybjCp Sigma70 -40.5 -61.5 ybjC, nfsA, rimK, ybjN
ttaattgctaAAAGCTATAACTGTTAAACAcaatacagtg
890842 890861 [GEA], [HIBSCS] [1]
  Rob activator zwfp Sigma70 -54.0 -115.5 zwf
gcttttcccgTAATCGCACGGGTGGATAAGcgtttacagt
1936420 1936439 [BPP] [5], [10]


Alignment and PSSM for Rob TFBSs    

Aligned TFBS of Rob   
  Sequence
 

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



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