RegulonDB RegulonDB 11.1: Operon Form
   

tolC-ygiBC operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit       
Name: tolC-ygiBC
Gene(s): tolC, ygiB, ygiC   Genome Browser M3D Gene expression COLOMBOS
Note(s): Method used to determine the Transcription Unit: RT-PCR analysis.
In a study where it was shown that the L-tryptophan eradicated persister cells, it was observed that the exogenous amino acid did not affect the expression of tolC, whereas it did affect other genes Li Y, Liu B, Guo J, Cong H, He S, Zhou H, Zhu F, Wang Q, Zhang L,2019.
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for ygiC. This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Dhamdhere G., et al., 2010
Promoter
Name: tolCp1
+1: 3178004
Distance from start of the gene: 111
Sequence: gtgaatttcagcgacgtttgactgccgtttgagcagtcatgtgttaaattgaggcacattAacgccctatggcacgtaacg
Note(s): Zhang et al. (2008) identified a new TSS for the tolCp1 promoter that is 5 nt upstream of the one identified by Eguchi et al. (2003) Zhang A,2008 Zhang et al. (2008) mentioned that the -10 box (TTAAAT) is better placed 6 nt distant from the TSS (transcriptional start site) they observed, and the TSS determined by Eguchi et al. (2003) is unusual since it is11 nt from the -10 box Zhang A,2008
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Eguchi Y., et al., 2003


Transcription unit          
Name: tolC-ygiBC
Gene(s): tolC, ygiB, ygiC   Genome Browser M3D Gene expression COLOMBOS
Note(s): In a study where it was shown that the L-tryptophan eradicated persister cells, it was observed that the exogenous amino acid did not affect the expression of tolC, whereas it did affect other genes Li Y, Liu B, Guo J, Cong H, He S, Zhou H, Zhu F, Wang Q, Zhang L,2019.
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for ygiC. This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Dhamdhere G., et al., 2010
Promoter
Name: tolCp2
+1: 3178012
Distance from start of the gene: 103
Sequence: cagcgacgtttgactgccgtttgagcagtcatgtgttaaattgaggcacattaacgccctAtggcacgtaacgccaacctt
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Eguchi Y., et al., 2003
TF binding sites (TFBSs)
[PhoP,+] 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 PhoP-phosphorylated activator tolCp2 3177958 3177975 -46.0 atttcagcgaCGTTTGACTGCCGTTTGAgcagtcatgt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [2]


Transcription unit          
Name: tolC-ygiBC
Gene(s): tolC, ygiB, ygiC   Genome Browser M3D Gene expression COLOMBOS
Note(s): One marbox can activate transcription of tolCp3 and tolCp4 expression through the MarA, SoxS and Rob transcriptional regulators. This marbox is unique among the known marA/soxS/rob regulon promoters Zhang A,2008
There is a consensus sequence for EnvgA in the upstream region of the tolC gene. In fact, increases in transcription of tolC from overproduction of EvgA have been mentioned by Masuda and Church (2002) and Nishino et al. (2003) Masuda N,2002. Nishino K,2003 However, Eguchi et al. (2003) showed reported that direct binding of EnvgA to the tolC promoter was not detected in their DNase I footprinting analysis (data not shown in the report) Eguchi Y,2003
In tolC mutants, the transcription levels of the marA/soxS/rob regulon and tolC itself are elevated. Based on these findingsis, Rosner and Martin (2009) inferred that the following homeostatic loop could be present in wild-type bacteria: (i) normal metabolism results in the generation of certain intracellular metabolites that trigger the upregulation of the transcriptional activators MarA, SoxS, and Rob; (ii) these transcriptional activators, in turn, upregulate tolC, increasing the capacity for excretion of the metabolites via TolC; and (iii) the resulting reduction in the concentrations of the trigger metabolites (TMs) restores the basal levels of the activators. In tolC, mutants, the metabolites are not as effectively excreted, and the activator levels remain elevated Rosner JL, Martin RG,2009
In a study where it was shown that the L-tryptophan eradicated persister cells, it was observed that the exogenous amino acid did not affect the expression of tolC, whereas it did affect other genes Li Y, Liu B, Guo J, Cong H, He S, Zhou H, Zhu F, Wang Q, Zhang L,2019.
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for ygiC. This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Dhamdhere G., et al., 2010
Promoter
Name: tolCp3
+1: 3178062
Distance from start of the gene: 53
Sequence: ttaacgccctatggcacgtaacgccaaccttttgcggtagcggcttctgctagaatccgcAataattttacagtttgatcg
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Zhang A., et al., 2008
TF binding sites (TFBSs)
[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 tolCp3 3178012 3178032 -40.5 ttaacgccctATGGCACGTAACGCCAACCTTttgcggtagc nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [3], [4], [5]
[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 tolCp3 3178012 3178032 -40.5 ttaacgccctATGGCACGTAACGCCAACCTTttgcggtagc nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [3], [4], [5]
[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 tolCp3 3178012 3178032 -40.5 ttaacgccctATGGCACGTAACGCCAACCTTttgcggtagc nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [3], [4], [5]


Transcription unit          
Name: tolC-ygiBC
Gene(s): tolC, ygiB, ygiC   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the tolC gene, and probably the expression of the complete tolC-ygiABC operon, is affected by tetracycline antibiotic pressure. An increase in tolC expression is maintained during exposition to increasing concentrations of tetracycline Viveiros M, Dupont M, Rodrigues L, Couto I, Davin-Regli A, Martins M, Pagès JM, Amaral L,2007
One marbox can activate transcription of tolCp3 and tolCp4 expression through the MarA, SoxS and Rob transcriptional regulators. This marbox is unique among the known marA/soxS/rob regulon promoters Zhang A,2008
There is a consensus sequence for EnvgA in the upstream region of the tolC gene. In fact, increases in transcription of tolC from overproduction of EvgA have been mentioned by Masuda and Church (2002) and Nishino et al. (2003) Masuda N,2002. Nishino K,2003 However, Eguchi et al. (2003) showed reported that direct binding of EnvgA to the tolC promoter was not detected in their DNase I footprinting analysis (data not shown in the report) Eguchi Y,2003
In tolC mutants, the transcription levels of the marA/soxS/rob regulon and tolC itself are elevated. Based on these findingsis, Rosner and Martin (2009) inferred that the following homeostatic loop could be present in wild-type bacteria: (i) normal metabolism results in the generation of certain intracellular metabolites that trigger the upregulation of the transcriptional activators MarA, SoxS, and Rob; (ii) these transcriptional activators, in turn, upregulate tolC, increasing the capacity for excretion of the metabolites via TolC; and (iii) the resulting reduction in the concentrations of the trigger metabolites (TMs) restores the basal levels of the activators. In tolC, mutants, the metabolites are not as effectively excreted, and the activator levels remain elevated Rosner JL, Martin RG,2009
In a study where it was shown that the L-tryptophan eradicated persister cells, it was observed that the exogenous amino acid did not affect the expression of tolC, whereas it did affect other genes Li Y, Liu B, Guo J, Cong H, He S, Zhou H, Zhu F, Wang Q, Zhang L,2019.
Review about the regulation of the tolC gene Weston N, Sharma P, Ricci V, Piddock LJV,2018.
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for ygiC. This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Dhamdhere G., et al., 2010
Promoter
Name: tolCp4
+1: 3178074
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 41
Sequence: ggcacgtaacgccaaccttttgcggtagcggcttctgctagaatccgcaataattttacaGtttgatcgcgctaaatactg
                          -35               -10             +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [6] Huerta AM., et al., 2003
[7] Salgado H, et al., 2012
[3] Zhang A., et al., 2008
TF binding sites (TFBSs)
[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 tolCp4 3178012 3178032 -52.5 ttaacgccctATGGCACGTAACGCCAACCTTttgcggtagc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [3], [4], [5]
[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 tolCp4 3178012 3178032 -52.5 ttaacgccctATGGCACGTAACGCCAACCTTttgcggtagc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [3]
[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 tolCp4 3178012 3178032 -52.5 ttaacgccctATGGCACGTAACGCCAACCTTttgcggtagc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [3]


Evidence    

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [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.

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

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates


Reference(s)    

 [1] Dhamdhere G., Zgurskaya HI., 2010, Metabolic shutdown in Escherichia coli cells lacking the outer membrane channel TolC., Mol Microbiol 77(3):743-54

 [2] Eguchi Y., Oshima T., Mori H., Aono R., Yamamoto K., Ishihama A., Utsumi R., 2003, Transcriptional regulation of drug efflux genes by EvgAS, a two-component system in Escherichia coli., Microbiology 149(Pt 10):2819-28

 [3] 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

 [4] 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

 [5] 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

 [6] 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

 [7] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [8] Parker A., Gottesman S., 2016, Small RNA Regulation of TolC, the Outer Membrane Component of Bacterial Multidrug Transporters., J Bacteriol 198(7):1101-13

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