RegulonDB RegulonDB 11.2: Operon Form
   

marRAB operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: marRAB
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: marRAB
Synonym(s): OP00264
Gene(s): marR, marA, marB   Genome Browser M3D Gene expression COLOMBOS
Note(s): There is a differential expression of the genes of the marRAB operon under antibiotic (tetracycline) pressure. While the expression of marA and marB is increased as the tetracycline concentration increases (from 1.5 to 10 mg/L), the expression of the marR gene is induced only at low concentrations (1.5 and 4 mg/L) Viveiros M, Dupont M, Rodrigues L, Couto I, Davin-Regli A, Martins M, Pagès JM, Amaral L,2007 marA gene expression is induced in the presence of menadione, salicylic acid, and norfloxacin in a MarR-dependent way Reyes-Fernández EZ, Schuldiner S,2020.
The proteins TolC and PAP I appear to be indirectly involved in the transcriptional regulation of marA and, thus, MarA-mediated multidrug resistance Ruiz C,2010 In the absence of TolC, the expression of marR was increased through CpxR/CpxA two-component regulatory system signal transduction and regulated the expression of AcrA/B in the AcrAB-TolC efflux pump Wang H, Zhang H, Zhang H, Jin J, Xie Y,2021
MarA increases activation of the marRp promoter in response to salicylate Chubiz LM, Glekas GD, Rao CV,2012 Salicylate activates the marRp promoter through Rob Chubiz LM, Glekas GD, Rao CV,2012Salicylate induces the marRp promoter independently of Mar, Sox, and Rob Chubiz LM, Glekas GD, Rao CV,2012 The marRp promoter had the highest expression in a marA soxS double mutant strain, compared to a marA single mutant and a marA rob double mutant strain, in the presence of salicylate Jain K, Saini S,2016
Both paraquat and decanoate activate the marRp promoter, in a SoxRS-dependent and Rob-dependent manner, respectively Chubiz LM, Glekas GD, Rao CV,2012 The expression of the marRp promoter activated by paraquat is higher when the MarR-dependent autorepression is relieved Jain K, Saini S,2016
The marRAB operon is induced instantaneously in response to (-)-roemerine, and this response continues for at least 60 minutes CITS:[ 28013396]|.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
[EXP-IEP] Inferred from expression pattern
[EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Cohen SP., et al., 1993
[2] Seoane AS., et al., 1995
Promoter
Name: marRp
+1: 1619093
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 27
Sequence: cgtggcatcggtcaattcattcatttgacttatacttgcctgggcaatattatcccctgcAactaattacttgccagggca
                         -35                    -10         +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA]
Reference(s): [3] Belliveau NM., et al., 2018
[1] Cohen SP., et al., 1993
[4] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[AcrR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal AcrR repressor marRp 1619048 1619058 -40.5 catcggtcaaTTCATTCATTTgacttatact nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [14]
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cyclic-AMP activator marRp 1619030 1619051 -52.5 cgatttagcaAAACGTGGCATCGGTCAATTCAttcatttgac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IMP], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [12], [13]
[CpxR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CpxR-phosphorylated activator marRp 1619057 1619072 -29.0 attcattcatTTGACTTATACTTGCCtgggcaatat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [15]
[Cra,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Cra repressor marRp 1619012 1619029 -72.5 attgaacaaaACTTGAACCGATTTAGCAaaacgtggca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ] S [6]
[Fis,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fis activator marRp 1619005 1619019 -81.0 gcatcgcattGAACAAAACTTGAACcgatttagca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-EXO], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [5]
[MarA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal MarA activator marRp 1619022 1619041 -61.5 acttgaaccgATTTAGCAAAACGTGGCATCggtcaattca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3], [8], [9], [10], [11]
[MarR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal MarR repressor marRp 1619064 1619085 -18.0 catttgacttATACTTGCCTGGGCAATATTATcccctgcaac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [2], [16], [17], [18], [19]
proximal MarR repressor marRp 1619098 1619119 17.0 cctgcaactaATTACTTGCCAGGGCAACTAATgtgaaaagta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [2], [16], [17], [18], [19]
[Rob,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Rob activator marRp 1619022 1619041 -61.5 acttgaaccgATTTAGCAAAACGTGGCATCggtcaattca nd [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 [5], [7], [8]
[SoxS,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal SoxS activator marRp 1619022 1619041 -61.5 acttgaaccgATTTAGCAAAACGTGGCATCggtcaattca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [8], [10]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [EXP-IDA] Inferred from direct assay

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IMP] Inferred from mutant phenotype

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing

 [EXP-CHIP-EXO] high throughput ChIP-exo evidence

 [EXP-CHIP-SEQ] high throughput ChIP-seq evidence

 [EXP-IMP-SITE-MUTATION] Site mutation

 [EXP-GSELEX] high throughput Genomic SELEX-chip evidence


Reference(s)    

 [1] 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

 [2] Seoane AS., Levy SB., 1995, Characterization of MarR, the repressor of the multiple antibiotic resistance (mar) operon in Escherichia coli., J Bacteriol 177(12):3414-9

 [3] Belliveau NM., Barnes SL., Ireland WT., Jones DL., Sweredoski MJ., Moradian A., Hess S., Kinney JB., Phillips R., 2018, Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria., Proc Natl Acad Sci U S A 115(21):E4796-E4805

 [4] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [5] 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

 [6] Shimada T., Yamamoto K., Ishihama A., 2011, Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli., J Bacteriol 193(3):649-59

 [7] 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

 [8] 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

 [9] Gillette WK., Martin RG., Rosner JL., 2000, Probing the Escherichia coli transcriptional activator MarA using alanine-scanning mutagenesis: residues important for DNA binding and activation., J Mol Biol 299(5):1245-55

 [10] 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

 [11] 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

 [12] Ruiz C., Levy SB., 2010, Many chromosomal genes modulate MarA-mediated multidrug resistance in Escherichia coli., Antimicrob Agents Chemother 54(5):2125-34

 [13] Zheng D., Constantinidou C., Hobman JL., Minchin SD., 2004, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling., Nucleic Acids Res 32(19):5874-93

 [14] Lee JO., Cho KS., Kim OB., 2014, Overproduction of AcrR increases organic solvent tolerance mediated by modulation of SoxS regulon in Escherichia coli., Appl Microbiol Biotechnol 98(20):8763-73

 [15] Weatherspoon-Griffin N., Yang D., Kong W., Hua Z., Shi Y., 2014, The CpxR/CpxA two-component regulatory system up-regulates the multidrug resistance cascade to facilitate Escherichia coli resistance to a model antimicrobial peptide., J Biol Chem 289(47):32571-82

 [16] Martin RG., Rosner JL., 2004, Transcriptional and translational regulation of the marRAB multiple antibiotic resistance operon in Escherichia coli., Mol Microbiol 53(1):183-91

 [17] Martin RG., Rosner JL., 1995, Binding of purified multiple antibiotic-resistance repressor protein (MarR) to mar operator sequences., Proc Natl Acad Sci U S A 92(12):5456-60

 [18] Notka F., Linde HJ., Dankesreiter A., Niller HH., Lehn N., 2002, A C-terminal 18 amino acid deletion in MarR in a clinical isolate of Escherichia coli reduces MarR binding properties and increases the MIC of ciprofloxacin., J Antimicrob Chemother 49(1):41-7

 [19] Shimada T., Ogasawara H., Ishihama A., 2018, Single-target regulators form a minor group of transcription factors in Escherichia coli K-12., Nucleic Acids Res 46(8):3921-3936

 [20] Wright PR., Richter AS., Papenfort K., Mann M., Vogel J., Hess WR., Backofen R., Georg J., 2013, Comparative genomics boosts target prediction for bacterial small RNAs., Proc Natl Acad Sci U S A 110(37):E3487-96

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