PA2093 is an extracytoplasmic function (ECF, group IV) sigma-70 family factor of Pseudomonas aeruginosa PAO1, with conserved sigma region 2 (promoter -10 recognition) and region 4 (-35 recognition) domains and membership of the FecI-like cell-surface signalling (CSS) subfamily. In CSS systems the sigma factor is held inactive by a cytoplasmic-membrane anti-sigma factor until an outer-membrane TonB-dependent transducer senses an extracellular signal; the freed sigma factor then binds RNA polymerase core in the cytoplasm and directs transcription of its target promoters. Overexpression of PA2093 induced a regulon that includes two TonB-dependent transducers and putative (metal) transport genes, so PA2093 is thought to control uptake of an as yet unidentified iron or metal carrier.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro2GO mapping of the sigma-70 domains to DNA-binding transcription factor activity. Reason: True but uninformative. In current GO, GO:0016987 sigma factor activity is_a GO:0003700, so the sigma factor activity accepted in this review entails this term. Supporting Evidence: file:PSEAE/PA2093/PA2093-uniprot.txt TIGR02937; sigma70-ECF file:PSEAE/PA2093/PA2093-uniprot.txt PF04542; Sigma70_r2 |
| GO:0005829 cytosol | NAS PMID:18086184 Characterization of five novel Pseudomonas aeruginosa cell-s... | ACCEPT | Summary: NAS location from the PseudoCAP-cited paper. ECF sigma factors of cell-surface signalling systems are cytoplasmic proteins sequestered by the inner-membrane anti-sigma factor and, once released, bind RNA polymerase in the cytoplasm. Reason: Where the sigma factor exerts its activity; consistent with the CSS model described in the paper. Supporting Evidence: PMID:18086184 This regulatory system consists of an outer membrane-localized TonB-dependent receptor (TonB-dependent transducer), a cytoplasmic membrane-localized antisigma factor and an extracytoplasmic function (ECF) sigma factor PMID:18086184 transmit them into the cytoplasm |
| GO:0006352 DNA-templated transcription initiation | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO transcription initiation from the sigma-70 domains. Reason: Sigma factors act in promoter recognition and open-complex formation during DNA-templated transcription initiation. Supporting Evidence: file:PSEAE/PA2093/PA2093-uniprot.txt TIGR02937; sigma70-ECF file:PSEAE/PA2093/PA2093-uniprot.txt PF04542; Sigma70_r2 |
| GO:0006355 regulation of DNA-templated transcription | IBA GO_REF:0000033 | TOO GENERAL | Summary: Regulation of DNA-templated transcription propagated from PTN002455017. Reason: True, but GO:2000142 regulation of DNA-templated transcription initiation, accepted on this gene, is an is_a descendant and entails it. |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | TOO GENERAL | Summary: Regulation of DNA-templated transcription from InterPro2GO. Reason: True, but GO:2000142 regulation of DNA-templated transcription initiation, accepted on this gene, is an is_a descendant and entails it. |
| GO:0016987 sigma factor activity | IBA GO_REF:0000033 | ACCEPT | Summary: Sigma factor activity propagated from PAINT node PTN002455017 (ECF sigma clade). The protein has the ECF sigma region 2 and region 4 domains, and this gene is itself one of the 16 IBD seeds through its own experimental row. Reason: Core function. The node is an ECF sigma factor clade whose IBD is grounded in many experimentally characterized members (E. coli FecI, Mtb SigE and SigL, S. coelicolor SigR, P. aeruginosa AlgU, PvdS, FpvI, SigX); the target's presence in WITH/FROM reflects its own experimental row, which is expected, not circular. Supporting Evidence: PMID:18086184 the ECF sigmas PA0149, PA1912, PA2050, PA2093 and PA4896 have been overexpressed and their target gene candidates have been identified using DNA microarray, proteomic analysis, and/or lacZ reporter construct file:PSEAE/PA2093/PA2093-uniprot.txt TIGR02937; sigma70-ECF file:PSEAE/PA2093/PA2093-uniprot.txt PF04542; Sigma70_r2 |
| GO:0016987 sigma factor activity | IMP PMID:18086184 Characterization of five novel Pseudomonas aeruginosa cell-s... | ACCEPT | Summary: PseudoCAP IMP seed for the PAINT IBD at PTN002455017. The abstract states that the sigma factor was overexpressed and its target genes identified by microarray, proteomics and/or lacZ reporters; overexpression falls under IMP. Reason: Seed verdict SOUND. Induction of specific target promoters by the sigma factor, together with an intact ECF sigma domain architecture, is the standard evidence for ECF sigma factor activity; it is the gene's own molecular function, not a downstream phenotype. Supporting Evidence: PMID:18086184 the ECF sigmas PA0149, PA1912, PA2050, PA2093 and PA4896 have been overexpressed and their target gene candidates have been identified using DNA microarray, proteomic analysis, and/or lacZ reporter construct PMID:18086184 two sigma factors, PA2050 and PA2093, regulate the synthesis of a second transducer |
| GO:0034756 regulation of iron ion transport | IMP PMID:18086184 Characterization of five novel Pseudomonas aeruginosa cell-s... | KEEP AS NON CORE | Summary: IMP from PMID:18086184 (abstract only). Overexpression induced TonB-dependent transducer and putative (metal) transport genes; the transported substrate is not stated in the abstract. Reason: Deferring to the curator, who read the full text: regulation of the transport genes is a transcriptional consequence of the sigma factor's activity, so it is a peripheral process. The substrate is described only as putative (metal), so a more specific or directional term is not justified from what could be read. Supporting Evidence: PMID:18086184 all these sigma factors seem to control putative (metal) transport systems |
| GO:2000142 regulation of DNA-templated transcription initiation | IEA GO_REF:0000108 | ACCEPT | Summary: Inferred from sigma factor activity by inter-ontology link. Reason: Directing RNA polymerase to specific promoters regulates transcription initiation; this is the most specific process term for the core activity. Supporting Evidence: PMID:18086184 the ECF sigmas PA0149, PA1912, PA2050, PA2093 and PA4896 have been overexpressed and their target gene candidates have been identified using DNA microarray, proteomic analysis, and/or lacZ reporter construct |
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Download this section (compressed HTML)Q: What extracellular signal activates the PA2093 cell-surface signalling system, and what does its regulated TonB-dependent transducer import?
Experiment: Screen candidate siderophores and metal carriers for induction of the PA2093 target TonB-dependent transducer promoter (lacZ or mCherry fusion) in wild type and a PA2093 deletion strain, then test uptake of the inducing carrier with 55Fe or other metal isotopes.
Type: reporter assay and isotope uptake
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