Np20 (PA5499), also called Zur, is the Fur-family zinc uptake regulator of Pseudomonas aeruginosa. It is encoded in an operon with znuC and znuB of the high-affinity ZnuABC zinc transporter. When zinc is plentiful, zinc-loaded Zur binds the znuA promoter and represses transcription of the zinc uptake genes; under zinc limitation repression is relieved. Loss of zur raises intracellular zinc. An np20 transposon mutant was also isolated as pyocyanin-deficient, with reduced expression of quorum-sensing-controlled genes, and np20 was earlier reported to be required for virulence in neutropenic mice.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000976 transcription cis-regulatory region binding | IBA GO_REF:0000033 | MODIFY | Summary: IBA from the PTN002112386 IBD (15 seeds, characterised Fur-family repressors). Reason: Correct and right for the node; for this gene, specific binding to the znuA promoter supports the child GO:0000987 cis-regulatory region sequence-specific DNA binding. Propagation Review Root cause: NO FAILURE CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN002112386 · PTN002112386 SUPPORTS TRANSFER Fur superfamily node (83 leaves). The DNA-binding IBDs rest on 15 characterised Fur, Zur and PerR repressors; node-level verdicts are in the fur notes. Proposed replacements: cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:24086521 Electrophoretic mobility shift assays also revealed that recombinant ZurPA specifically binds to the promoter region of znuA and does not bind in the presence of the zinc chelator |
| GO:0003677 DNA binding | IDA PMID:24086521 The transcriptional regulator Np20 is the zinc uptake regula... | MODIFY | Summary: PseudoCAP IDA; EMSA shows specific, zinc-dependent binding to the znuA promoter. Reason: Correct but general; specific promoter binding supports GO:0000987. Proposed replacements: cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:24086521 Electrophoretic mobility shift assays also revealed that recombinant ZurPA specifically binds to the promoter region of znuA and does not bind in the presence of the zinc chelator |
| GO:0003700 DNA-binding transcription factor activity | IBA GO_REF:0000033 | MODIFY | Summary: IBA from the PTN002112386 IBD (15 seeds). Reason: Correct for the node; the gene-level evidence (promoter binding plus loss of repression in the mutant) supports GO:0001217 DNA-binding transcription repressor activity. Propagation Review Root cause: NO FAILURE CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN002112386 · PTN002112386 SUPPORTS TRANSFER GO:0003700 IBD rests on 15 characterised Fur-family repressors and stands without any single seed. Proposed replacements: DNA-binding transcription repressor activity Supporting Evidence: PMID:24086521 Electrophoretic mobility shift assays also revealed that recombinant ZurPA specifically binds to the promoter region of znuA and does not bind in the presence of the zinc chelator PMID:24086521 transcription of znuA was repressed in a zinc-dependent manner in strain PAO1, however zinc-dependent transcriptional repression was alleviated in strain PAO-Zur |
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping from the Fur domain. Reason: Correct but general; the gene-level evidence supports GO:0001217. Proposed replacements: DNA-binding transcription repressor activity Supporting Evidence: PMID:24086521 Electrophoretic mobility shift assays also revealed that recombinant ZurPA specifically binds to the promoter region of znuA and does not bind in the presence of the zinc chelator PMID:24086521 transcription of znuA was repressed in a zinc-dependent manner in strain PAO1, however zinc-dependent transcriptional repression was alleviated in strain PAO-Zur |
| GO:0005829 cytosol | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA cytosol from PTN002112441 (seed E. coli Fur). Reason: A soluble cytoplasmic DNA-binding repressor; cytosol is plausible and the location is peripheral to the function. Supporting Evidence: PMID:24086521 Electrophoretic mobility shift assays also revealed that recombinant ZurPA specifically binds to the promoter region of znuA and does not bind in the presence of the zinc chelator |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro2GO mapping. Reason: GO:0045892 negative regulation of DNA-templated transcription, accepted in this review, is_a GO:0006355. Supporting Evidence: PMID:24086521 transcription of znuA was repressed in a zinc-dependent manner in strain PAO1, however zinc-dependent transcriptional repression was alleviated in strain PAO-Zur |
| GO:0006882 intracellular zinc ion homeostasis | IMP PMID:24086521 The transcriptional regulator Np20 is the zinc uptake regula... | ACCEPT | Summary: PseudoCAP IMP; Δzur cells accumulate more intracellular zinc. Reason: Zur controls zinc import in response to zinc levels, so it acts in maintaining intracellular zinc; supported by the mutant's elevated zinc. Supporting Evidence: PMID:24086521 Intracellular zinc concentrations in strain PAO-Zur (Δzur) were found to be higher than those for strain PAO1 |
| GO:0008270 zinc ion binding | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN002112386 (seeds E. coli Fur and M. tuberculosis Zur). Reason: Zur binds structural and regulatory zinc; DNA binding by Np20 is lost when zinc is chelated, and the PIRSR zinc site is conserved. Supporting Evidence: PMID:24086521 Electrophoretic mobility shift assays also revealed that recombinant ZurPA specifically binds to the promoter region of znuA and does not bind in the presence of the zinc chelator file:PSEAE/np20/np20-uniprot.txt Binds 1 zinc ion per subunit. |
| GO:0045892 negative regulation of DNA-templated transcription | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the PTN002112386 IBD (16 seeds); np20 is one of them, which is expected, not circular. The IBD stands on the other 15. Reason: Core BP; Zur represses znuA transcription in a zinc-dependent manner. Supporting Evidence: PMID:24086521 transcription of znuA was repressed in a zinc-dependent manner in strain PAO1, however zinc-dependent transcriptional repression was alleviated in strain PAO-Zur |
| GO:0045892 negative regulation of DNA-templated transcription | IDA PMID:24086521 The transcriptional regulator Np20 is the zinc uptake regula... | ACCEPT | Summary: PseudoCAP IDA and one of 16 seeds of the PTN002112386 GO:0045892 IBD. Zinc-dependent repression of znuA lost in the zur mutant, with direct promoter binding. Seed verdict SOUND. Reason: Core BP, directly demonstrated. Supporting Evidence: PMID:24086521 transcription of znuA was repressed in a zinc-dependent manner in strain PAO1, however zinc-dependent transcriptional repression was alleviated in strain PAO-Zur PMID:24086521 Electrophoretic mobility shift assays also revealed that recombinant ZurPA specifically binds to the promoter region of znuA and does not bind in the presence of the zinc chelator |
| GO:0071294 cellular response to zinc ion | IMP PMID:24086521 The transcriptional regulator Np20 is the zinc uptake regula... | ACCEPT | Summary: PseudoCAP IMP; zinc-dependent repression of znuA requires Zur. Reason: Zur is the zinc sensor that mediates the transcriptional response to zinc. Supporting Evidence: PMID:24086521 transcription of znuA was repressed in a zinc-dependent manner in strain PAO1, however zinc-dependent transcriptional repression was alleviated in strain PAO-Zur |
| GO:0071579 regulation of zinc ion transport | IMP PMID:24086521 The transcriptional regulator Np20 is the zinc uptake regula... | ACCEPT | Summary: PseudoCAP IMP; Zur represses the znuABC zinc uptake genes. Reason: Acceptable under the convention that a transcription factor is annotated to regulation of the process its target genes carry out; Zur controls expression of the ZnuABC zinc importer. Supporting Evidence: PMID:24086521 transcription of znuA was repressed in a zinc-dependent manner in strain PAO1, however zinc-dependent transcriptional repression was alleviated in strain PAO-Zur |
| GO:1900376 regulation of secondary metabolite biosynthetic process | IBA GO_REF:0000033 | REMOVE | Summary: IBA from the PTN002112386 GO:1900376 IBD, whose two seeds are this gene (an indirect mutant phenotype) and P. aeruginosa Fur (negative regulation of siderophore biosynthesis). Reason: The np20 seed is an indirect, pleiotropic phenotype, and Fur's siderophore control is specific to iron regulators; the node spans the whole Fur superfamily (Fur, Zur, PerR, Irr and others). Nothing shows that Zur regulates secondary-metabolite biosynthesis. The node-level GO_CENTRAL defect is already recorded on the fur review (genes/PSEAE/fur, GO:1900705 row) and is not duplicated here. Propagation Review Root cause: SOURCE BAD Failure modes: SOURCE EVIDENCE WEAK LINEAGE OR TAXON MISMATCH Sources checked: PANTHER:PTN002112386 · PTN002112386 SOURCE BAD Fur superfamily node (71 leaf IBAs for this term, 33 taxa); a Fur-lineage regulatory output placed at a superfamily node. See the fur notes for the GO_CENTRAL defect. UniProtKB:Q9HT74 · np20 (self; PseudoCAP IMP PMID:12426334) SOURCE BAD Indirect transposon-mutant phenotype (reduced pyocyanin); see the IMP row. UniProtKB:Q03456 · P. aeruginosa Fur SUPPORTS SOURCE BUT NOT TARGET Fur represses siderophore biosynthesis via PvdS and PchR; this does not transfer to Zur. Supporting Evidence: PMID:12426334 Third, mutations in the putative regulators np20 and PA3946 reduced transcription of a number of quorum sensing-controlled genes, showing that these functions participate in the quorum-sensing regulatory network. PMID:24086521 transcription of znuA was repressed in a zinc-dependent manner in strain PAO1, however zinc-dependent transcriptional repression was alleviated in strain PAO-Zur |
| GO:1900376 regulation of secondary metabolite biosynthetic process | IMP PMID:12426334 Functions required for extracellular quinolone signaling by ... | REMOVE | Summary: PseudoCAP IMP and one of two seeds of the PTN002112386 GO:1900376 IBD. An np20 transposon mutant was isolated as pyocyanin-deficient and had reduced expression of quorum-sensing-controlled genes. Seed verdict INDIRECT-PHENOTYPE. Reason: The paper reports a pleiotropic mutant phenotype without any mechanism; Np20's demonstrated function is zinc-responsive repression of zinc uptake genes. The lower pyocyanin is most likely a downstream consequence of disturbed zinc homeostasis or quorum-sensing output, not regulation of phenazine biosynthesis by Np20. Supporting Evidence: PMID:12426334 Third, mutations in the putative regulators np20 and PA3946 reduced transcription of a number of quorum sensing-controlled genes, showing that these functions participate in the quorum-sensing regulatory network. PMID:24086521 transcription of znuA was repressed in a zinc-dependent manner in strain PAO1, however zinc-dependent transcriptional repression was alleviated in strain PAO-Zur |
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Download this section (compressed HTML)Q: How does loss of Np20/Zur reduce pyocyanin production and quorum-sensing gene expression: through zinc excess, through Zur-regulated paralogs (for example zinc-independent ribosomal proteins), or through a direct Zur target in the quorum-sensing network?
Experiment: ChIP-seq of Zur under zinc-replete conditions to define its direct regulon, combined with pyocyanin and pqsA reporter measurements in Δzur with and without zinc chelation.
Type: ChIP-seq / reporter assay
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