MexZ (PA2020) is a TetR-family transcriptional repressor that controls the mexXY operon, encoding the MexXY multidrug efflux pump that gives Pseudomonas aeruginosa intrinsic resistance to aminoglycosides. MexZ binds as a dimer to a 20-bp palindromic operator in the mexZ-mexX intergenic region and represses mexXY. Ribosome-targeting antibiotics induce the anti-repressor ArmZ (PA5471), which binds the N-terminal DNA-binding domain of MexZ, reduces MexZ binding to DNA and so derepresses mexXY. mexZ is among the genes most frequently mutated in cystic fibrosis isolates, where its loss causes MexXY overproduction and moderate aminoglycoside resistance.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000976 transcription cis-regulatory region binding | IBA GO_REF:0000033 | MODIFY | Summary: IBA from PTN004738546; MexZ is itself a seed of this IBD, which is expected, not circular. MexZ binds a 20-bp palindrome in the mexZ-mexX intergenic region. Reason: Correct but general. Binding to a defined palindromic operator supports the child GO:0000987 cis-regulatory region sequence-specific DNA binding, which the gene already carries by IDA. 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 node; 19 seeds for GO:0006355 (7 for GO:0000976, 7 for GO:0003700), most of them experimentally characterised TetR regulators. The node-level verdict is recorded on the nfxB/nalC/PA3678/atuR/nalD reviews. UniProtKB:G3XCU9 · mexZ (self; PseudoCAP, CollecTF and UniProt experimental rows) SUPPORTS TRANSFER Expected self-seed reflecting the target's own experimental evidence. Proposed replacements: cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:19589837 MexZ binds to a 20 bp palindromic sequence PMID:15336398 Highly purified MexZ showed direct binding with a specific site of the mexZ-mexX intergenic DNA when probed by a gel retardation assay |
| GO:0000976 transcription cis-regulatory region binding | IMP PMID:19589837 Role of MexZ and PA5471 in transcriptional regulation of mex... | MODIFY | Summary: CollecTF row from the EMSA and repression study. MexZ binds the mexXY promoter region. Reason: Same claim as the IBA row; sequence-specific operator binding supports GO:0000987. The binding itself is an EMSA result, so IDA would be a better code than IMP. Proposed replacements: cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:19589837 MexZ binds to a 20 bp palindromic sequence PMID:15336398 Highly purified MexZ showed direct binding with a specific site of the mexZ-mexX intergenic DNA when probed by a gel retardation assay |
| GO:0000987 cis-regulatory region sequence-specific DNA binding | IDA PMID:31527038 Interaction of ArmZ with the DNA-binding domain of MexZ indu... | ACCEPT | Summary: EMSA with purified MexZ-His6 and the mexXY-mexZ intergenic region. Reason: Direct binding to the mexXY promoter at a defined palindromic site; core MF. Supporting Evidence: PMID:31527038 The impact of ArmZ on MexZ binding to DNA in vitro was analyzed using an electrophoretic mobility shift assay (EMSA) with purified MexZ-His 6 and the mexXY-mexZ intergenic region ( mexXY p) as a probe PMID:19589837 MexZ binds to a 20 bp palindromic sequence |
| GO:0001217 DNA-binding transcription repressor activity | IMP PMID:19589837 Role of MexZ and PA5471 in transcriptional regulation of mex... | ACCEPT | Summary: Plasmid-borne MexZ represses drug-induced MexX production; MexZ binds the mexXY operator. Reason: Repression plus direct operator binding shows DNA-binding transcription repressor activity; core MF. Supporting Evidence: PMID:19589837 the plasmid-borne MexZ repressed drug-induced MexX production, further confirming that MexZ acts as a repressor of the mexXY operon PMID:19589837 MexZ binds to a 20 bp palindromic sequence |
| GO:0001217 DNA-binding transcription repressor activity | IMP PMID:31527038 Interaction of ArmZ with the DNA-binding domain of MexZ indu... | ACCEPT | Summary: MexZ variants were tested for repression of the mexXY promoter; MexZ is the mexXY repressor. Reason: Consistent with the other repressor-activity rows; core MF. Supporting Evidence: PMID:31527038 The expression of mexXY operon is negatively regulated by MexZ repressor. |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO from the TetR HTH domain. True. Reason: DNA binding is correct but general; the gene has experimental support for GO:0000987. Proposed replacements: cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:19589837 MexZ binds to a 20 bp palindromic sequence |
| GO:0003700 DNA-binding transcription factor activity | IBA GO_REF:0000033 | MODIFY | Summary: IBA from PTN004738546; MexZ is a seed. MexZ is a DNA-binding repressor. Reason: Correct but general; the gene-level evidence supports GO:0001217 DNA-binding transcription repressor activity, already carried by IMP. 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 node; 19 seeds for GO:0006355 (7 for GO:0000976, 7 for GO:0003700), most of them experimentally characterised TetR regulators. The node-level verdict is recorded on the nfxB/nalC/PA3678/atuR/nalD reviews. UniProtKB:G3XCU9 · mexZ (self; PseudoCAP, CollecTF and UniProt experimental rows) SUPPORTS TRANSFER Expected self-seed reflecting the target's own experimental evidence. Proposed replacements: DNA-binding transcription repressor activity Supporting Evidence: PMID:19589837 the plasmid-borne MexZ repressed drug-induced MexX production, further confirming that MexZ acts as a repressor of the mexXY operon PMID:19589837 MexZ binds to a 20 bp palindromic sequence |
| GO:0005515 protein binding | IPI PMID:19589837 Role of MexZ and PA5471 in transcriptional regulation of mex... | REMOVE | Summary: Yeast two-hybrid interaction of MexZ with the anti-repressor ArmZ (PA5471, Q9HT99). Reason: Bare protein binding is uninformative and is removed under the protein-binding policy. The interaction is real: ArmZ binds MexZ and reduces its DNA binding. MexZ is the target of the anti-repressor, not an inhibitor itself, so no more informative MF term applies to MexZ. Supporting Evidence: PMID:19589837 interaction between PA5471 and MexZ reduced MexZ DNA-binding ability, leading to mexXY transcription |
| GO:0005515 protein binding | IPI PMID:31527038 Interaction of ArmZ with the DNA-binding domain of MexZ indu... | REMOVE | Summary: Bacterial two-hybrid and pull-down interaction of MexZ with ArmZ (Q9HT99), mapped to the MexZ N-terminal DNA-binding domain. Reason: Bare protein binding is uninformative and is removed under the protein-binding policy. The interaction is real and is described in the core function. Supporting Evidence: PMID:31527038 the N-terminal part of MexZ, encompassing the DNA-binding domain, is required for interaction with ArmZ |
| GO:0006355 regulation of DNA-templated transcription | IBA GO_REF:0000033 | MODIFY | Summary: IBA from the PTN004738546 IBD (19 seeds). MexZ 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 MexZ is a repressor; GO:0045892 is supported and already carried by several experimental rows. Propagation Review Root cause: NO FAILURE CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN004738546 · PTN004738546 SUPPORTS TRANSFER TetR-family node; 19 seeds for GO:0006355 (7 for GO:0000976, 7 for GO:0003700), most of them experimentally characterised TetR regulators. The node-level verdict is recorded on the nfxB/nalC/PA3678/atuR/nalD reviews. UniProtKB:G3XCU9 · mexZ (self; PseudoCAP, CollecTF and UniProt experimental rows) SUPPORTS TRANSFER Expected self-seed reflecting the target's own experimental evidence. Proposed replacements: negative regulation of DNA-templated transcription Supporting Evidence: PMID:23441219 In a mutant strain lacking the mexZ gene encoding a repressor of mexXY gene expression, expression of the efflux operon increases modestly (5-fold) PMID:19589837 the plasmid-borne MexZ repressed drug-induced MexX production, further confirming that MexZ acts as a repressor of the mexXY operon |
| GO:0006355 regulation of DNA-templated transcription | IDA PMID:15336398 MexZ-mediated regulation of mexXY multidrug efflux pump expr... | MODIFY | Summary: PseudoCAP IDA and one of 19 seeds of the PTN004738546 IBD. The abstract reports that purified MexZ binds a specific site in the mexZ-mexX intergenic DNA (gel retardation) and that this explains MexZ repression of mexXY. The seed is sound. Reason: Sound but under-specific. The paper (and the same-paper PseudoCAP IMP row) supports GO:0045892 negative regulation of DNA-templated transcription. A descendant term still supports the generic IBD. Proposed replacements: negative regulation of DNA-templated transcription Supporting Evidence: PMID:15336398 Highly purified MexZ showed direct binding with a specific site of the mexZ-mexX intergenic DNA when probed by a gel retardation assay PMID:15336398 These results explain the mechanism by which MexZ represses transcription of the mexXY operon |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000117 | MODIFY | Summary: ARBA machine-learning row for regulation of transcription. True. Reason: Same claim as the IBA and IDA rows; the experimental evidence supports GO:0045892. Proposed replacements: negative regulation of DNA-templated transcription Supporting Evidence: PMID:23441219 In a mutant strain lacking the mexZ gene encoding a repressor of mexXY gene expression, expression of the efflux operon increases modestly (5-fold) |
| GO:0032410 negative regulation of transporter activity | IMP PMID:15105120 Role of the multidrug efflux system MexXY in the emergence o... | REMOVE | Summary: PseudoCAP IMP from a study of mexZ alterations in aminoglycoside-resistant CF isolates. Complementation with mexZ lowered MICs and MexY overproduction is associated with mexZ alterations. Reason: GO:0032410 is a process that reduces the activity of a transporter. MexZ represses transcription of mexXY and so lowers the amount of the pump. The abstract itself names mexZ as the repressor gene of the operon and gives no sign that MexZ acts on the MexXY protein. The correct process is captured by the negative regulation of transcription rows and by GO:1905700. Supporting Evidence: PMID:15105120 Alterations in mexZ, the repressor gene of operon mexXY, were found in all of the AG-resistant CF isolates PMID:15105120 Complementation of these bacteria with a plasmid-borne mexZ gene dramatically reduced the MICs of AGs |
| GO:0032993 protein-DNA complex | IMP PMID:19589837 Role of MexZ and PA5471 in transcriptional regulation of mex... | KEEP AS NON CORE | Summary: CollecTF row for the MexZ-operator complex, from EMSA of MexZ on the mexXY promoter. Reason: MexZ forms a protein-DNA complex on its operator, as the EMSA data show. This is a CollecTF convention, true but peripheral to the core function. Supporting Evidence: PMID:19589837 MexZ binds to a 20 bp palindromic sequence |
| GO:0034763 negative regulation of transmembrane transport | IMP PMID:15105120 Role of the multidrug efflux system MexXY in the emergence o... | MODIFY | Summary: PseudoCAP IMP. mexZ alterations cause MexXY overproduction and lower intracellular aminoglycoside accumulation, reversed by mexZ complementation. Reason: Acceptable under the GO convention that a transcription factor is annotated to the process its target genes carry out. The target, MexXY, exports aminoglycosides, so the more specific descendant GO:1905700 fits. Non-core. Proposed replacements: negative regulation of xenobiotic detoxification by transmembrane export across the plasma membrane Supporting Evidence: PMID:15105120 Complementation of these bacteria with a plasmid-borne mexZ gene dramatically reduced the MICs of AGs PMID:15105120 Alterations in mexZ, the repressor gene of operon mexXY, were found in all of the AG-resistant CF isolates |
| GO:0045892 negative regulation of DNA-templated transcription | IDA PMID:19589837 Role of MexZ and PA5471 in transcriptional regulation of mex... | ACCEPT | Summary: CollecTF IDA; EMSA and in vitro transcription with MexZ and ArmZ. Reason: Direct binding and repression of mexXY; core process. Supporting Evidence: PMID:19589837 the plasmid-borne MexZ repressed drug-induced MexX production, further confirming that MexZ acts as a repressor of the mexXY operon PMID:19589837 interaction between PA5471 and MexZ reduced MexZ DNA-binding ability, leading to mexXY transcription |
| GO:0045892 negative regulation of DNA-templated transcription | IEP PMID:19589837 Role of MexZ and PA5471 in transcriptional regulation of mex... | ACCEPT | Summary: CollecTF IEP; MexZ and MexX levels rise with tetracycline. Reason: The claim is true and core, as shown by the other rows on this term. IEP is a weak code for a regulatory claim, since an expression pattern cannot by itself show that MexZ represses transcription. Supporting Evidence: PMID:19589837 the plasmid-borne MexZ repressed drug-induced MexX production, further confirming that MexZ acts as a repressor of the mexXY operon |
| GO:0045892 negative regulation of DNA-templated transcription | IMP PMID:15336398 MexZ-mediated regulation of mexXY multidrug efflux pump expr... | ACCEPT | Summary: PseudoCAP IMP from the same paper as the seed IDA; MexZ binding to the intergenic operator explains repression of mexXY. Reason: Core process, consistent with all other rows on this term. Supporting Evidence: PMID:15336398 These results explain the mechanism by which MexZ represses transcription of the mexXY operon |
| GO:0045892 negative regulation of DNA-templated transcription | IMP PMID:23441219 Antibiotic inducibility of the mexXY multidrug efflux operon... | ACCEPT | Summary: Deletion of mexZ raises mexXY expression about 5-fold. Reason: Direct genetic evidence for repression; core process. Supporting Evidence: PMID:23441219 In a mutant strain lacking the mexZ gene encoding a repressor of mexXY gene expression, expression of the efflux operon increases modestly (5-fold) |
| GO:0045892 negative regulation of DNA-templated transcription | IMP PMID:31527038 Interaction of ArmZ with the DNA-binding domain of MexZ indu... | ACCEPT | Summary: MexZ represses the mexXY promoter; ArmZ-interface mutants retain repression. Reason: Core process. Supporting Evidence: PMID:31527038 The expression of mexXY operon is negatively regulated by MexZ repressor. |
| GO:0046677 response to antibiotic | IMP PMID:23441219 Antibiotic inducibility of the mexXY multidrug efflux operon... | KEEP AS NON CORE | Summary: Antibiotic induction of mexXY depends on relief of MexZ repression by ArmZ; ArmZ mutants that cannot relieve MexZ are pan-aminoglycoside-susceptible. Reason: MexZ is part of the antibiotic-inducible mexXY response, acting as the repressor that ArmZ relieves. This is a valid but downstream physiological role, not the core activity. Supporting Evidence: PMID:23441219 rendering the mutants pan-aminoglycoside-susceptible PMID:19589837 interaction between PA5471 and MexZ reduced MexZ DNA-binding ability, leading to mexXY transcription |
| GO:0046677 response to antibiotic | IMP PMID:31527038 Interaction of ArmZ with the DNA-binding domain of MexZ indu... | KEEP AS NON CORE | Summary: A MexZ K53E variant that cannot bind ArmZ blocks tetracycline induction of mexY and makes cells more aminoglycoside-susceptible. Reason: Same as the other response to antibiotic row; non-core. Supporting Evidence: PMID:31527038 Concomitantly, PAO1161 mexZ K53E strain was more susceptible to aminoglycosides. |
| GO:1990837 sequence-specific double-stranded DNA binding | IDA PMID:15336398 MexZ-mediated regulation of mexXY multidrug efflux pump expr... | MODIFY | Summary: Gel retardation shows MexZ binding to a specific site in the mexZ-mexX intergenic DNA. Reason: Correct but general; the site is a promoter operator, so GO:0000987 (a descendant, already carried by IDA) is the specific term. Proposed replacements: cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:15336398 Highly purified MexZ showed direct binding with a specific site of the mexZ-mexX intergenic DNA when probed by a gel retardation assay |
| GO:1990837 sequence-specific double-stranded DNA binding | IDA PMID:20691272 Crystal structure of MexZ, a key repressor responsible for a... | MODIFY | Summary: Crystal structure of MexZ combined with DNA-binding data on mutants. Reason: Correct but general; GO:0000987 is the specific term for MexZ operator binding. Proposed replacements: cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:20691272 Combining the structural information with biochemical data on key mutants identified, we provide an explanation for the structural and functional consequences of these mutants PMID:19589837 MexZ binds to a 20 bp palindromic sequence |
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Download this section (compressed HTML)Q: Does MexZ bind any small-molecule ligand in its C-terminal domain, or is it regulated solely by protein interaction with ArmZ?
Q: Which other promoters, besides mexXY and its own, does MexZ regulate in vivo?
Experiment: ChIP-seq of MexZ in PAO1 with and without sub-inhibitory aminoglycoside, and a ligand screen (thermal shift) on purified MexZ.
Type: ChIP-seq and ligand screening
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