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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 [19] These proteins activate a common set of about 50 target genes [1, 20, 21, 22] the marA/soxS/rob regulon, involved in antibiotic resistance [14, 23, 24] superoxide resistance [7, 25, 26] and tolerance to organic solvents [27, 28, 29]and heavy metals [30] The activity of each protein is induced by different signals: the activity of Rob is increased with dipyridyl, bile salts, or decanoate [2, 31] and the activities of MarA and SoxS are increased by the aromatic weak acid salicylate [22]and oxidative stress [32] respectively.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
Rob Functional   nd nd nd
Evolutionary Family: AraC/XylS
TFBs length: 20
TFBs symmetry: asymmetric
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, aldA, aslB, chaC, elaB, fadA, fadB, fadL, fumC, inaA, ldtB, marA, marB, marR, micF, mltF, nfo, nfsA, nfsB, rimK, rob, sodA, tolC, ybjC, ybjN, ygiB, ygiC, yiaG, zwf
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
drug resistance/sensitivity (7)
adaptations (3)
fatty acids (3)
Transcription related (3)
detoxification (3)
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Regulated operon(s) acrAB, acrZ, aldA, aslB, chaBC, elaB, fadBA, fadL, fumAC, inaA, ldtB, marRAB, micF, mltF, nfo, nfsB, rob, sodA, tolC-ygiBC, ybjC-nfsA-rimK-ybjN, yiaG, ymiC-acnA, zwf
First gene in the operon(s) acnA, acrA, acrZ, aldA, aslB, chaC, elaB, fadB, fadL, fumC, inaA, ldtB, marR, micF, mltF, nfo, nfsB, rob, sodA, tolC, ybjC, yiaG, 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,DnaA,FNR,MarA,Rob,SoxS
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Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[Rob,-](5)
[Rob,+](20)


Transcription factor regulation    


Transcription factor binding sites (TFBSs) arrangements
      

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence
LeftPos RightPos Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
  Rob activator acnAp2 Sigma70 -51.5 -101.5 acnA
aaggtttctcCTCTTTTATCAATTTGGGTTgttatcaaat
1335720 1335739 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1], [1]
  Rob activator acrAp Sigma70 nd nd acrA, acrB nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2]
  Rob activator acrZp Sigma70 -40.5 -62.5 acrZ
cgcaaagctgACCGCACAAAAGGGGAGTGCttttctgtgc
794701 794720 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF], [EXP-CHIP-EXO] S [3], [3], [4]
  Rob activator aldAp Sigma70 -161.0 -203.0 aldA
gcgatggaaaGTCGCTCGTTACGTTAAAAAttgcccgttt
1488019 1488038 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [1], [1]
  Rob activator aslBp Sigma54 nd nd aslB nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [5]
  Rob activator chaCp Sigma54 nd nd chaC nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [6]
  Rob repressor elaBp Sigma38 nd nd elaB nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [6]
  Rob repressor fadBp Sigma70 nd nd fadB, fadA nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [6]
  Rob repressor fadLp Sigma38 nd nd fadL nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [6]
  Rob activator fumCp1 Sigma70 -35.5 -101.5 fumC
gtttttttacATGGCACGAAAGACCAAACAtttgttatca
1686680 1686699 [EXP-IEP], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-EXO], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [4], [7], [7], [8], [8]
  Rob activator inaAp Sigma70 -41.5 -68.5 inaA
attcattaatACGACACGTTTCATTAAGATtttcctcagg
2349531 2349550 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [5], [6], [9]
  Rob activator ldtBp nd nd nd ldtB nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [5]
  Rob activator marRp Sigma70 -61.5 -88.5 marR, marA, marB
acttgaaccgATTTAGCAAAACGTGGCATCggtcaattca
1619022 1619041 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4], [5], [5], [9], [10], [11]
  Rob activator micFp1 Sigma70 -40.0 -40.0 micF
aagtatttgaCAGCACTGAATGTCAAAACAaaaccttcac
2313034 2313053 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [4], [11], [12], [12], [13]
  Rob activator micFp2 Sigma38 -40.0 -40.0 micF
aagtatttgaCAGCACTGAATGTCAAAACAaaaccttcac
2313034 2313053 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [4], [11], [12], [12], [13]
  Rob activator mltFp Sigma70 nd nd mltF nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [5]
  Rob activator nfop Sigma70 -38.5 -72.5 nfo
tcaaagcgtcATCGCATAAACCACTACATCttgctcctgt
2250758 2250777 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [9], [14]
  Rob activator nfsBp Sigma70 -43.5 -72.5 nfsB
gcggaaatctATAGCGCATTTTTCTCGCTTaccatttctc
605487 605506 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1], [1]
  Rob repressor robp nd -19.5 -62.5 rob
actgaatgctAAAACAGCAAAAAATGCTATtatccaatta
4635363 4635382 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [4], [11], [15], [15]
  Rob activator sodAp Sigma70 -40.5 -91.5 sodA
tacgaaaagtACGGCATTGATAATCATTTTcaatatcatt
4100709 4100728 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO] W [4], [14]
  Rob activator tolCp3 nd -40.5 -93.5 tolC, ygiB, ygiC
ttaacgccctATGGCACGTAACGCCAACCTTttgcggtagc
3178012 3178032 [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO] S [4], [16], [16], [17], [17], [18], [18]
  Rob activator tolCp4 Sigma38 -52.5 -93.5 tolC, ygiB, ygiC
ttaacgccctATGGCACGTAACGCCAACCTTttgcggtagc
3178012 3178032 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO] S [4], [16], [17], [18], [18]
  Rob activator ybjCp Sigma70 -40.5 -61.5 ybjC, nfsA, rimK, ybjN
ttaattgctaAAAGCTATAACTGTTAAACAcaatacagtg
890842 890861 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1], [1]
  Rob repressor yiaGp Sigma38 nd nd yiaG nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [6]
  Rob activator zwfp Sigma70 -54.0 -116.0 zwf
gcttttcccgTAATCGCACGGGTGGATAAGcgtttacagt
1936420 1936439 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [7], [7], [14]



High-throughput Transcription factor binding sites (TFBSs)
      

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Center Position Growth Condition Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
  Rob activator mdaB Transcription-Unit nd
cgcaaaagacTTTGCACATTTTGCTAATTTcaccgtaccg
3172452 3172471 3172462.0 nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ] S [1]
  Rob activator map-glnD-dapD Transcription-Unit nd
aatcattctgAATTTCGCCAAACGTGCCACtgaaggtttt
189597 189616 189607.0 nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [1]
  Rob activator yhbW Transcription-Unit nd
gcctaagtaaATAGCTCACTTTGTTAACAActttaactac
3303372 3303391 3303382.0 nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [1]
  Rob activator yacH Transcription-Unit nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [6]
  Rob activator narG Gene nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [6]
  Rob activator ydcL Transcription-Unit nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [6]
  Rob activator mdtD Gene nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [6]
  Rob activator ybiT Transcription-Unit nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [6]
  Rob activator glgS Gene nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [6]
  Rob repressor acs Gene nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [6]
  Rob repressor yhbO Transcription-Unit nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [6]
  Rob repressor yjcH Gene nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [6]
  Rob repressor astC Gene nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [6]
  Rob repressor actP Gene nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [6]
  Rob repressor fadD Gene nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [6]


Alignment and PSSM for Rob TFBSs    

Aligned TFBS of Rob   
  Sequence
  AGGTTGGCGTTACGTGCCATAGG
  GTTTTGACATTCAGTGCTGTCAA
  GATTTAGCAAAACGTGGCATCGG
  TGTTTGGTCTTTCGTGCCATGTA
  ATAATAGCATTTTTTGCTGTTTT
  CGCTTATCCACCCGTGCGATTAC
  ATCTTAATGAAACGTGTCGTATT
  TTTTTAACGTAACGAGCGACTTT
  CTTTTATCAATTTGGGTTGTTAT
  GCACTCCCCTTTTGTGCGGTCAG
  GATGTAGTGGTTTATGCGATGAC
  TGTTTAACAGTTATAGCTTTTAG
  AAAATGATTATCAATGCCGTACT
  AAGCGAGAAAAATGCGCTATAGA

Position weight matrix (PWM). Rob matrix-quality result   
A	5	4	3	2	0	9	5	1	6	6	4	5	3	2	2	0	0	0	7	0	4	6	3
C	2	1	2	2	0	1	1	9	3	0	1	3	6	0	1	0	11	5	0	1	3	1	2
G	4	4	2	1	1	4	6	0	4	2	0	0	0	10	1	14	1	4	6	0	2	3	4
T	3	5	7	9	13	0	2	4	1	6	9	6	5	2	10	0	2	5	1	13	5	4	5

Consensus   
;	consensus.strict             	ggttTagCaattcGtGCcgTtag
;	consensus.strict.rc          	CTAACGGCACGAATTGCTAAACC
;	consensus.IUPAC              	rkttTrrCvwthyGtGCbrTyrk
;	consensus.IUPAC.rc           	MYRAYVGCACRDAWBGYYAAAMY
;	consensus.regexp             	[ag][gt]ttT[ag][ag]C[acg][at]t[act][ct]GtGC[cgt][ag]T[ct][ag][gt]
;	consensus.regexp.rc          	[AC][CT][AG]A[CT][ACG]GCAC[AG][AGT]A[AT][CGT]G[CT][CT]AAA[AC][CT]

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




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] Decker KT, Gao Y, Rychel K, Al Bulushi T, Chauhan SM, Kim D, Cho BK, Palsson BO, 2022, proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms., Nucleic Acids Res, 50(D1):D1077 10.1093/nar/gkab1043

 [5] 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

 [6] 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

 [7] 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

 [8] 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 σ(70) Subunit of RNA Polymerase., J Mol Biol 419(3-4):139-57

 [9] 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

 [10] 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

 [11] Baumgart LA, Lee JE, Salamov A, Dilworth DJ, Na H, Mingay M, Blow MJ, Zhang Y, Yoshinaga Y, Daum CG, O'Malley RC, 2021, Persistence and plasticity in bacterial gene regulation., Nat Methods, 18(12):1499 10.1038/s41592-021-01312-2

 [12] 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

 [13] Zhang C., Chen S., Dedkova LM., Hecht SM., 2020, Effects of Nucleobase Amino Acids on the Binding of Rob to Its Promoter DNA: Differential Alteration of DNA Affinity and Phenotype., Biochemistry 59(22):2111-2119

 [14] 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

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

 [16] 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

 [17] 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

 [18] 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

 [19] 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

 [20] 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 10.1128/JB.182.12.3467-3474.2000

 [21] Martin RG, Rosner JL, 2003, Analysis of microarray data for the marA, soxS, and rob regulons of Escherichia coli., Methods Enzymol, 370(None):278 10.1016/S0076-6879(03)70024-X

 [22] 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

 [23] 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

 [24] 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 10.1111/j.1365-2958.2005.04599.x

 [25] 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

 [26] Wu J, Weiss B, 1992, Two-stage induction of the soxRS (superoxide response) regulon of Escherichia coli., J Bacteriol, 174(12):3915 10.1128/jb.174.12.3915-3920.1992

 [27] 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 10.1128/jb.179.19.6122-6126.1997

 [28] Aono R, 1998, Improvement of organic solvent tolerance level of Escherichia coli by overexpression of stress-responsive genes., Extremophiles, 2(3):239 10.1007/s007920050066

 [29] He X, Xue T, Ma Y, Zhang J, Wang Z, Hong J, Hui L, Qiao J, Song H, Zhang M, 2019, Identification of functional butanol-tolerant genes from Escherichia coli mutants derived from error-prone PCR-based whole-genome shuffling., Biotechnol Biofuels, 12(None):73 10.1186/s13068-019-1405-z

 [30] 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 10.1128/aem.61.6.2302-2307.1995

 [31] 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 10.1128/JB.184.5.1407-1416.2002

 [32] Demple B, 1996, Redox signaling and gene control in the Escherichia coli soxRS oxidative stress regulon--a review., Gene, 179(1):53 10.1016/s0378-1119(96)00329-0

 [33] 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 10.1128/JB.00680-12

 [34] 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

 [35] 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

 [36] 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

 [37] 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

 [38] 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 10.1006/bbrc.2002.6559

 [39] 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 10.1046/j.1365-2958.2002.02748.x

 [40] 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

 [41] 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 10.1016/s0022-2836(02)00782-9

 [42] 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 10.1073/pnas.95.18.10413

 [43] Corbella M, Liao Q, Moreira C, Parracino A, Kasson PM, Kamerlin SCL, 2021, The N-terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition., J Phys Chem B, 125(25):6791 10.1021/acs.jpcb.1c00771

 [44] Rodgers ME, Schleif R, 2009, Solution structure of the DNA binding domain of AraC protein., Proteins, 77(1):202 10.1002/prot.22431

 [45] 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 10.1016/j.jmb.2009.03.023

 [46] 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

 [47] 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 10.1128/JB.181.20.6361-6370.1999

 [48] 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 10.1007/BF02423459

 [49] Zhang C., Chen S., Bai X., Dedkova LM., Hecht SM., 2020, Alteration of Transcriptional Regulator Rob In Vivo: Enhancement of Promoter DNA Binding and Antibiotic Resistance in the Presence of Nucleobase Amino Acids., Biochemistry 59(12):1217-1220

 [50] Zhang C, Chen S, Dedkova LM, Hecht SM, 2020, Effects of Nucleobase Amino Acids on the Binding of Rob to Its Promoter DNA: Differential Alteration of DNA Affinity and Phenotype., Biochemistry, 59(22):2111 10.1021/acs.biochem.0c00290

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