Transcription Factor

						

			
Accessions: ECK120005810 (RegulonDB 7.5)

			
Names: Rob, Rob DNA-binding transcriptional activator
Organisms: ECK12
Libraries: RegulonDB 7.5 1
1 Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muniz-Rascado L, Garcia-Sotelo JS, Weiss V, Solano-Lira H, Martinez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernandez S, Alquicira-Hernandez K, Lopez-Fuentes A, Porron-Sotelo L, Huerta AM, Bonavides-Martinez C, Balderas-Martinez YI, Pannier L, Olvera M, Labastida A, Jimenez-Jacinto V, Vega-Alvarado L, Del Moral-Chavez V, Hernandez-Alvarez A, Morett E, Collado-Vides J. RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucleic Acids Res. 2013 Jan 1;41(D1):D203-D213. [Pubmed]
Notes: Rob is a transcriptional dual regulator; Its N-terminal domain shares 49% identity with MarA and SoxS Cohen SP,1993 These proteins activate a common set of about 50 target genes Barbosa TM,2000; Martin RG,2002; Martin RG,2003; Pomposiello PJ,2001 the marA/soxS/rob regulon, involved in antibiotic resistance Martin RG,1996; Griffith KL,2005; Ariza RR,1995 superoxide resistance Jair KW,1996; Nunoshiba T,1992; Wu J,1992 and tolerance to organic solvents White DG,1997; Aono R.,1998and heavy metals Nakajima H,1995 The activity of each protein is induced by different signals: the activity of Rob is increased with dipyridyl, bile salts, or decanoate Rosner JL,2002; Rosenberg EY,2003 and the activities of MarA and SoxS are increased by the aromatic weak acid salicylate Pomposiello PJ,2001and oxidative stress Demple B.,1996 respectively; 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 Pomposiello PJ,2003 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 Martin RG,1999; Wood TI,1999 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 Martin RG,1999; Wood TI,1999 As a subset of the class I promoters, the Mar-Sox-Rob box is separated by ~30 bp from the -10 hexamer but can be functional in either orientation Martin RG,1999; Wood TI,1999The Mar-Sox-Rob box contains an invariant A at position 1, two recognition elements, the RE1 at position 4-7 and RE2 at position 15-18, and a 7-bp A/T-rich spacer separating these elements Kwon HJ,2000; Dangi B,2001; Griffith KL,2001 There are more than 10,000 such 
binding sites per genome Griffith KL,2002 However, the majority of these sites are not functional because they are not in the proper orientation or distance relative to the promoter Martin RG,2002 It was proposed that these proteins bind to their target sites by a mechanism named DNA scanning or prerecruitment; In prerecruitment, the protein first binds to RNA polymerase in solution, and the binary complex then scans the DNA to find its binding sites Martin RG,2002; Griffith KL,2002 Rob consists of two domains and belongs to the AraC/XylS family Gallegos MT,1997 The N-terminal domain is the DNA-binding domain and is homologous to MarA and SoxS and the C-terminal domain of AraC; It carries two helix-turn-helix (HTH) motifs for DNA binding; One of them, located in the N-terminal region, interacts with the element RE1 of the Mar-Sox-Rob box, and the HTH located in the C-terminal region interacts with RE2 Griffith KL,2002; Rhee S,1998; Dangi B,2001 In the case of Rob, it appears that only one of the two HTH 
motifs makes base-specific contacts with DNA Kwon HJ,2000 The crystal structures of Rob Kwon HJ,2000and MarA Rhee S,1998in complex with DNA and the solution structure of the DNA-binding domain of AraC Rodgers ME,2009have been solved.The C-terminal domain of Rob is similar to a portion of the enzyme GalT Kwon HJ,2000 It regulates the activity of Rob by a sequestration-disposal mechanism, that is, it mediates the sequestration of Rob into intracellular foci; Sequestered Rob is inactive; Upon addition of the inducer, Rob is released in its active form Griffith KL,2009 The C-terminal domain blocks in addition proteolytic degradation by Lon protease Griffith KL,2009rob appears to be transcribed abundantly at 5,000-10,000 molecules per cell Skarstad K,1993; Ali Azam T,1999 throughout the growth cycle; rob expression is enhanced at the stationary phase and under glucose and phosphate starvation, and it was suggested that expression of rob is σS dependent Kakeda M,1995 Reviews: Alekshun MN,1999; Demple B.,1996;
 Randall LP,2002; DNA replication; Transcription related; nucleoproteins, basic proteins; activator; regulon; cytoplasm; sequence-specific DNA binding; intracellular; sequence-specific DNA binding transcription factor activity; DNA binding; DNA-dependent DNA replication; regulation of transcription, DNA-dependent
Length: 290
Pfam Domains:    27-105 Helix-turn-helix domain
   69-105 Bacterial regulatory helix-turn-helix proteins, AraC family
  127-288 GyrI-like small molecule binding domain
Sequence: 
(in bold interface residues)		   1 MDQAGIIRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAIGAYIRARRLS   60
  61 KSAVALRLTARPILDIALQYRFDSQQTFTRAFKKQFAQTPALYRRSPEWSAFGIRPPLRL  120
 121 GEFTMPEHKFVTLEDTPLIGVTQSYSCSLEQISDFRHEMRYQFWHDFLGNAPTIPPVLYG  180
 181 LNETRPSQDKDDEQEVFYTTALAQDQADGYVLTGHPVMLQGGEYVMFTYEGLGTGVQEFI  240
 241 LTVYGTCMPMLNLTRRKGQDIERYYPAEDAKAGDRPINLRCELLIPIRR*
Interface Residues: 34, 35, 36, 37, 39, 40, 43, 51, 85, 86, 89, 90, 94
3D-footprint Homologues: 3w6v_A, 7vwz_G, 1zgw_A, 1xs9_A
Binding Motifs: Rob AyrGCAckdawyrhyAA
Binding Sites: ECK120011192
ECK120011418
ECK120017109
ECK120051567
ECK120051581
ECK120051610
			
Publications: Rodgers ME., Schleif R. Solution structure of the DNA binding domain of AraC protein. Proteins. 77(1):202-8 (2009). [Pubmed]


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


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


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


Nunoshiba T., Hidalgo E., Amabile Cuevas CF., Demple B. 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 (1992). [Pubmed]


White DG., Goldman JD., Demple B., Levy SB. 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 (1997). [Pubmed]


Cohen SP., Hachler H., Levy SB. Genetic and functional analysis of the multiple antibiotic resistance (mar) locus in Escherichia coli. J Bacteriol. 175(5):1484-92 (1993). [Pubmed]


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


Martin RG., Rosner JL. 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 (2002). [Pubmed]


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


Pomposiello PJ., Bennik MH., Demple B. Genome-wide transcriptional profiling of the Escherichia coli responses to superoxide stress and sodium salicylate. J Bacteriol. 183(13):3890-902 (2001). [Pubmed]


Martin RG., Jair KW., Wolf RE., Rosner JL. Autoactivation of the marRAB multiple antibiotic resistance operon by the MarA transcriptional activator in Escherichia coli. J Bacteriol. 178(8):2216-23 (1996). [Pubmed]


Griffith KL., Becker SM., Wolf RE. 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 (2005). [Pubmed]


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


Jair KW., Yu X., Skarstad K., Thony B., Fujita N., Ishihama A., Wolf RE. 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 (1996). [Pubmed]


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


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


Nakajima H., Kobayashi K., Kobayashi M., Asako H., Aono R. 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 (1995). [Pubmed]


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


Rosenberg EY., Bertenthal D., Nilles ML., Bertrand KP., Nikaido H. 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 (2003). [Pubmed]


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


Martin RG., Gillette WK., Rhee S., Rosner JL. 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 (1999). [Pubmed]


Wood TI., Griffith KL., Fawcett WP., Jair KW., Schneider TD., Wolf RE. 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 (1999). [Pubmed]


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


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


Griffith KL., Wolf RE. 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 (2001). [Pubmed]


Griffith KL., Shah IM., Myers TE., O'Neill MC., Wolf RE. 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 (2002). [Pubmed]


Martin RG., Gillette WK., Martin NI., Rosner JL. 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 (2002). [Pubmed]


Griffith KL., Wolf RE. 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 (2002). [Pubmed]


Rhee S., Martin RG., Rosner JL., Davies DR. 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 (1998). [Pubmed]


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


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


Kakeda M., Ueguchi C., Yamada H., Mizuno T. 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 (1995). [Pubmed]


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


Griffith KL., Fitzpatrick MM., Keen EF., Wolf RE. 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 (2009). [Pubmed]
Related annotations: PaperBLAST

	
			


			

				

				
				
				
				

			

			

		

	
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