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| Operon |  |
|---|---|
| Name: | tolC-ygiBC |
| This page displays every known transcription unit of this operon and their known regulation. | |
| 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: | [LTED] 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: | [TIM] |
| Reference(s): | [2] Eguchi Y., et al., 2003 |
| 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. |
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| Evidence: | [LTED] 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 |
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| Evidence: | [TIM] | |||||||||
| Reference(s): | [2] Eguchi Y., et al., 2003 | |||||||||
| Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
| proximal | PhoP-phosphorylated | activator | tolCp2 | 3177958 | 3177975 | -46.0 | atttcagcgaCGTTTGACTGCCGTTTGAgcagtcatgt | nd | [GEA], [APIORCISFBSCS] | [2] |
| 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. |
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| Evidence: | [LTED] 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 |
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| Evidence: | [TIM] | |||||||||
| Reference(s): | [3] Zhang A., et al., 2008 | |||||||||
| Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
| proximal | MarA | activator | tolCp3 | 3178012 | 3178032 | -40.5 | ttaacgccctATGGCACGTAACGCCAACCTtttgcggtag | nd | [AIBSCS], [GEA], [AIBSCS] | [3], [4], [5] |
| Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
| proximal | Rob | activator | tolCp3 | 3178012 | 3178032 | -40.5 | ttaacgccctATGGCACGTAACGCCAACCTtttgcggtag | nd | [AIBSCS], [GEA], [AIBSCS] | [3], [4], [5] |
| Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
| proximal | SoxS | activator | tolCp3 | 3178012 | 3178032 | -40.5 | ttaacgccctATGGCACGTAACGCCAACCTtttgcggtag | nd | [AIBSCS], [GEA], [AIBSCS] | [3], [4], [5] |
| 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: | [LTED] 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: |
[AIPP] [ICWHO] [RS-EPT-CBR] [TIM] |
| Reference(s): |
[6] Huerta AM., et al., 2003 [7] Salgado H, et al., 2012 [3] Zhang A., et al., 2008 |
| Reference(s) |
|
|---|---|
[TIM] Transcription initiation mapping