FoxI (PA2468) is the extracytoplasmic function (ECF) sigma factor of the Fox cell-surface signalling system of Pseudomonas aeruginosa PAO1, which lets the bacterium use the heterologous hydroxamate siderophore ferrioxamine B. FoxI has the sigma-70 region 2 and region 4 domains of the FecI-like ECF subfamily. It is encoded in the Fur-repressed foxI-foxR operon next to foxA, the ferrioxamine TonB-dependent receptor. Without ferrioxamine, FoxI is held inactive by the transmembrane anti-sigma factor FoxR. Binding of ferrioxamine to FoxA triggers proteolytic processing of FoxR, which releases FoxI to direct RNA polymerase to the foxA promoter. FoxI overexpression strongly induces foxA transcription and FoxA production, which in turn mediates ferric-ferrioxamine uptake.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003677 DNA binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO DNA binding from the sigma-70 region 4 domain. Reason: True by homology (ECF sigma region 4 contacts the -35 promoter element), but no direct DNA-binding assay exists for this protein, so a more specific DNA-binding term is not warranted. The informative MF is sigma factor activity. Supporting Evidence: file:PSEAE/foxI/foxI-uniprot.txt PF08281; Sigma70_r4_2 |
| 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/foxI/foxI-uniprot.txt TIGR02937; sigma70-ECF file:PSEAE/foxI/foxI-uniprot.txt PF04542; Sigma70_r2 |
| GO:0005829 cytosol | NAS PMID:16484199 The heterologous siderophores ferrioxamine B and ferrichrome... | 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:16484199 both receptor genes are located next to a regulatory locus encoding an extracytoplasmic function sigma factor and a transmembrane sensor |
| 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/foxI/foxI-uniprot.txt TIGR02937; sigma70-ECF file:PSEAE/foxI/foxI-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:16484199 The involvement of this putative regulatory locus in the specific induction of the ferrioxamine B and ferrichrome receptors has been demonstrated file:PSEAE/foxI/foxI-uniprot.txt TIGR02937; sigma70-ECF file:PSEAE/foxI/foxI-uniprot.txt PF04542; Sigma70_r2 |
| GO:0016987 sigma factor activity | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO sigma factor activity from the sigma-70 region 4 type 2 domain. Reason: Consistent with the IBA and IMP rows; the ECF sigma domain architecture is complete. Supporting Evidence: file:PSEAE/foxI/foxI-uniprot.txt TIGR02937; sigma70-ECF file:PSEAE/foxI/foxI-uniprot.txt PF04542; Sigma70_r2 file:PSEAE/foxI/foxI-uniprot.txt PF08281; Sigma70_r4_2 |
| GO:0016987 sigma factor activity | IMP PMID:16484199 The heterologous siderophores ferrioxamine B and ferrichrome... | ACCEPT | Summary: PseudoCAP IMP seed for the PAINT IBD at PTN002455017. The full text (PMC1426570, read for this review) shows that constitutive expression of the sigma factor from a plasmid induces transcription from the cognate receptor promoter (lacZ fusion) and production of the receptor protein; no foxI mutant was tested, so the evidence is overexpression, which GO accepts 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:16484199 The involvement of this putative regulatory locus in the specific induction of the ferrioxamine B and ferrichrome receptors has been demonstrated PMID:16484199 both receptor genes are located next to a regulatory locus encoding an extracytoplasmic function sigma factor and a transmembrane sensor PMID:25809487 This regulatory pathway controls the transcription of the foxA ferrioxamine receptor gene through the extracytoplasmic function sigma factor Ο(FoxI) |
| GO:0034756 regulation of iron ion transport | IMP PMID:16484199 The heterologous siderophores ferrioxamine B and ferrichrome... | MODIFY | Summary: IMP from the PseudoCAP-cited paper. The sigma factor drives transcription of the cognate TonB-dependent siderophore receptor gene, and that receptor imports the ferric siderophore, so the sigma factor positively regulates siderophore-mediated iron uptake. Reason: Correct, but the direction is known: the sigma factor induces receptor expression (full text of PMC1426570), so the specific term is GO:0034758 positive regulation of iron ion transport. Non-core: it is a consequence of the transcriptional activity on one target gene. Proposed replacements: positive regulation of iron ion transport Supporting Evidence: PMID:16484199 The involvement of this putative regulatory locus in the specific induction of the ferrioxamine B and ferrichrome receptors has been demonstrated PMID:39138320 Iron complexed by desferioxamine G is transported by FpvB and FoxA, ferricrocin-Fe and ferrichrycin-Fe by FpvB and FiuA |
| 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:16484199 The involvement of this putative regulatory locus in the specific induction of the ferrioxamine B and ferrichrome receptors has been demonstrated |
Loading supporting contentβ¦
Download this section (compressed HTML)Q: Does the sigma factor bind its target promoter directly as part of RNA polymerase holoenzyme (in vitro transcription or ChIP), and does its regulon extend beyond the receptor gene?
Loading supporting contentβ¦
Download this section (compressed HTML)Loading supporting contentβ¦
Download this section (compressed HTML)