PA3678 encodes MexL, a TetR-family transcriptional repressor of Pseudomonas aeruginosa that controls the divergently transcribed mexJK operon, encoding the MexJK RND efflux system (which exports triclosan and, with OprM, tetracycline and erythromycin), and its own gene. MexL is a tetramer in solution and binds the 94-bp mexL-mexJ intergenic region, protecting about 60 nucleotides that overlap both promoters and contain two inverted GTATTT repeats. Mutations in the helix-turn-helix region (such as A47D) abolish DNA binding and cause constitutive mexJK expression and triclosan resistance.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000976 transcription cis-regulatory region binding | IBA GO_REF:0000033 | MODIFY | Summary: IBA from the PTN004738546 IBD (7 seeds). PA3678 sits inside this TetR clade and is itself a seed, which is expected, not circular. PA3678 binds an inverted-repeat operator in its target promoter. Reason: Correct and appropriate for the node, but binding to a defined inverted-repeat operator supports the child GO:0000987 cis-regulatory region sequence-specific DNA binding for this gene (the same refinement used for mexZ, which shares the node). The generic term stays right for the node. Propagation Review Root cause: NO FAILURE CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN004738546 · PTN004738546 SUPPORTS TRANSFER TetR-family PAINT node (411 leaf IBAs, 33 taxa). Its IBDs rest on 19 seeds for GO:0006355, 7 for GO:0000976 and 7 for GO:0003700, including E. coli AcrR (P0ACS9, IDA operator binding and DNA-binding TF activity), RutR (P0ACU2), Vibrio VC_1746 (Q9KR96) and M. tuberculosis KstR, Mce3R and EthR. The generic node terms suit a TetR clade and stand without any single seed; node-level verdict recorded in the nfxB notes. UniProtKB:Q9HXW2 · PA3678 (self; experimental seed) SUPPORTS TRANSFER Expected self-seed reflecting the target's own experimental evidence; not circular. Proposed replacements: cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:15855505 Gel mobility shift and footprinting assays demonstrated that MexL, but not MexL(A47D), binds specifically to the 94-bp mexL-mexJ intergenic region |
| GO:0000976 transcription cis-regulatory region binding | IPI PMID:15855505 Molecular characterization of MexL, the transcriptional repr... | MODIFY | Summary: CollecTF row from the same gel shift and footprinting data. Reason: Same claim as the IBA and IDA rows; sequence-specific binding supports GO:0000987. Purified-protein binding would better be coded IDA. Proposed replacements: cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:15855505 Gel mobility shift and footprinting assays demonstrated that MexL, but not MexL(A47D), binds specifically to the 94-bp mexL-mexJ intergenic region |
| GO:0001217 DNA-binding transcription repressor activity | IPI PMID:15855505 Molecular characterization of MexL, the transcriptional repr... | ACCEPT | Summary: CollecTF row: MexL binds the mexL-mexJ region and regulates mexL and mexJK fusions. Reason: DNA binding plus repression of target-promoter fusions; core MF. Supporting Evidence: PMID:15855505 Gel mobility shift and footprinting assays demonstrated that MexL, but not MexL(A47D), binds specifically to the 94-bp mexL-mexJ intergenic region PMID:15855505 consistent with MexL regulating the expression of both mexL and mexJK, which was ascertained by gene fusion analyses PMID:12193619 Expression of this operon is negatively regulated by the product of mexL, a gene located upstream of and transcribed divergently from mexJK |
| GO:0003677 DNA binding | IEA GO_REF:0000120 | MODIFY | Summary: InterPro/UniRule mapping from the TetR HTH (TetR_N) domain. True. Reason: DNA binding is correct but general; PA3678 binds a defined operator, which supports GO:0000987. Proposed replacements: cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:15855505 Gel mobility shift and footprinting assays demonstrated that MexL, but not MexL(A47D), binds specifically to the 94-bp mexL-mexJ intergenic region |
| GO:0003700 DNA-binding transcription factor activity | IBA GO_REF:0000033 | MODIFY | Summary: IBA from the PTN004738546 IBD (7 seeds). PA3678 is a DNA-binding TetR-family repressor. Reason: Correct but general. The gene-level evidence (operator binding plus derepression in the mutant) supports GO:0001217 DNA-binding transcription repressor activity. The generic term remains right for the node. Propagation Review Root cause: NO FAILURE CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN004738546 · PTN004738546 SUPPORTS TRANSFER TetR-family PAINT node (411 leaf IBAs, 33 taxa). Its IBDs rest on 19 seeds for GO:0006355, 7 for GO:0000976 and 7 for GO:0003700, including E. coli AcrR (P0ACS9, IDA operator binding and DNA-binding TF activity), RutR (P0ACU2), Vibrio VC_1746 (Q9KR96) and M. tuberculosis KstR, Mce3R and EthR. The generic node terms suit a TetR clade and stand without any single seed; node-level verdict recorded in the nfxB notes. UniProtKB:Q9HXW2 · PA3678 (self; experimental seed) SUPPORTS TRANSFER Expected self-seed reflecting the target's own experimental evidence; not circular. Proposed replacements: DNA-binding transcription repressor activity Supporting Evidence: PMID:15855505 Gel mobility shift and footprinting assays demonstrated that MexL, but not MexL(A47D), binds specifically to the 94-bp mexL-mexJ intergenic region PMID:12193619 Expression of this operon is negatively regulated by the product of mexL, a gene located upstream of and transcribed divergently from mexJK PMID:15855505 consistent with MexL regulating the expression of both mexL and mexJK, which was ascertained by gene fusion analyses |
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO (IPR050109 TetR-like regulator) mapping. True. Reason: Correct but general; the gene-level evidence supports GO:0001217 DNA-binding transcription repressor activity. Proposed replacements: DNA-binding transcription repressor activity Supporting Evidence: PMID:15855505 Gel mobility shift and footprinting assays demonstrated that MexL, but not MexL(A47D), binds specifically to the 94-bp mexL-mexJ intergenic region PMID:12193619 Expression of this operon is negatively regulated by the product of mexL, a gene located upstream of and transcribed divergently from mexJK PMID:15855505 consistent with MexL regulating the expression of both mexL and mexJK, which was ascertained by gene fusion analyses |
| GO:0006355 regulation of DNA-templated transcription | IBA GO_REF:0000033 | MODIFY | Summary: IBA from the PTN004738546 IBD (19 seeds). PA3678 is one of them, which is expected, not circular. The IBD stands on the other 18 seeds as well. Reason: Correct and appropriate for the node, but PA3678 is a repressor; GO:0045892 negative regulation of DNA-templated transcription is supported by the gene's own experimental rows. Propagation Review Root cause: NO FAILURE CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN004738546 · PTN004738546 SUPPORTS TRANSFER TetR-family PAINT node (411 leaf IBAs, 33 taxa). Its IBDs rest on 19 seeds for GO:0006355, 7 for GO:0000976 and 7 for GO:0003700, including E. coli AcrR (P0ACS9, IDA operator binding and DNA-binding TF activity), RutR (P0ACU2), Vibrio VC_1746 (Q9KR96) and M. tuberculosis KstR, Mce3R and EthR. The generic node terms suit a TetR clade and stand without any single seed; node-level verdict recorded in the nfxB notes. UniProtKB:Q9HXW2 · PA3678 (self; experimental seed) SUPPORTS TRANSFER Expected self-seed reflecting the target's own experimental evidence; not circular. Proposed replacements: negative regulation of DNA-templated transcription Supporting Evidence: PMID:12193619 Expression of this operon is negatively regulated by the product of mexL, a gene located upstream of and transcribed divergently from mexJK PMID:15855505 consistent with MexL regulating the expression of both mexL and mexJK, which was ascertained by gene fusion analyses |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO (IPR050109) mapping. True. Reason: Correct but general; PA3678 is shown to be a repressor, so GO:0045892 applies. Proposed replacements: negative regulation of DNA-templated transcription Supporting Evidence: PMID:12193619 Expression of this operon is negatively regulated by the product of mexL, a gene located upstream of and transcribed divergently from mexJK PMID:15855505 consistent with MexL regulating the expression of both mexL and mexJK, which was ascertained by gene fusion analyses |
| GO:0032993 protein-DNA complex | IPI PMID:15855505 Molecular characterization of MexL, the transcriptional repr... | KEEP AS NON CORE | Summary: CollecTF row for the MexL-operator complex. Reason: True (footprinting shows the complex) but a peripheral CollecTF convention. Supporting Evidence: PMID:15855505 Gel mobility shift and footprinting assays demonstrated that MexL, but not MexL(A47D), binds specifically to the 94-bp mexL-mexJ intergenic region |
| GO:0043565 sequence-specific DNA binding | IDA PMID:15855505 Molecular characterization of MexL, the transcriptional repr... | MODIFY | Summary: PseudoCAP IDA: gel shift and footprinting of purified MexL on the mexL-mexJ intergenic region. Reason: Correct; binding to a defined promoter-overlapping site is more precisely GO:0000987 cis-regulatory region sequence-specific DNA binding. Proposed replacements: cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:15855505 Gel mobility shift and footprinting assays demonstrated that MexL, but not MexL(A47D), binds specifically to the 94-bp mexL-mexJ intergenic region |
| GO:0045892 negative regulation of DNA-templated transcription | IMP PMID:12193619 The MexJK efflux pump of Pseudomonas aeruginosa requires Opr... | ACCEPT | Summary: PseudoCAP IMP and one of the 19 seeds of the PTN004738546 GO:0006355 IBD. The abstract states that mexL negatively regulates mexJK and that a triclosan-resistant mutant carries an HTH substitution in MexL. Seed verdict SOUND. Reason: Direct repressor of mexJK and of mexL (confirmed with gene fusions and footprinting in PMID:15855505); core BP. Supporting Evidence: PMID:12193619 Expression of this operon is negatively regulated by the product of mexL, a gene located upstream of and transcribed divergently from mexJK PMID:15855505 consistent with MexL regulating the expression of both mexL and mexJK, which was ascertained by gene fusion analyses |
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Download this section (compressed HTML)Q: What ligand (for example triclosan or a natural substrate of MexJK) binds MexL and induces mexJK?
Experiment: Test candidate MexJK substrates for release of MexL from the mexL-mexJ operator by EMSA.
Type: ligand screening
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