FpvI (PA2387) is an iron-starvation extracytoplasmic function (ECF) sigma factor of Pseudomonas aeruginosa PAO1 that directs transcription of fpvA, which encodes the ferri-pyoverdine outer membrane receptor. fpvI is Fur-repressed in iron-replete cells. FpvI activity is held in check by the inner-membrane anti-sigma factor FpvR, which also controls PvdS. Binding of ferri-pyoverdine to FpvA signals across the envelope to FpvR and greatly increases FpvI activity, so pyoverdine induces its own receptor. FpvI has the sigma-70 region 2 and region 4.2 modules of the FecI-like ECF group and acts as the promoter-specificity subunit of RNA polymerase.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003677 DNA binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro region 4.2 helix-turn-helix mapping. Sigma factors contact promoter DNA (region 4.2 at -35, region 2 at -10), but they do so within the RNA polymerase holoenzyme. Reason: True, and as precise as domain-only evidence allows for a sigma subunit, whose DNA contacts are part of the holoenzyme's promoter recognition captured by GO:0016987. It is not a separate core activity. Supporting Evidence: file:PSEAE/fpvI/fpvI-uniprot.txt PF04542; Sigma70_r2 |
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro mapping to DNA-binding transcription factor activity. In current GO, GO:0016987 sigma factor activity is_a GO:0003700, so this term is entailed by the sigma factor activity accepted in this review. Reason: True but uninformative; GO:0016987, accepted here, entails it. Supporting Evidence: file:PSEAE/fpvI/fpvI-uniprot.txt PF04542; Sigma70_r2 |
| GO:0006352 DNA-templated transcription initiation | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro sigma-70 mapping to transcription initiation, the step at which sigma factors act. Reason: Sigma factors take part in initiation itself (promoter recognition and open complex formation); core process. Supporting Evidence: PMID:19730690 Sigma factors are essential subunits of prokaryotic RNA polymerase, they are involved in promoter recognition and transcription initiation file:PSEAE/fpvI/fpvI-uniprot.txt PF04542; Sigma70_r2 |
| GO:0006355 regulation of DNA-templated transcription | IBA GO_REF:0000033 | MODIFY | Summary: IBA from the PAINT IBD on PTN002455017 (8 seeds, including PvdS and AlgU). Regulation of transcription is true of every ECF sigma factor, and fpvI sits inside the clade. Reason: Correct but general. A sigma factor regulates transcription at the initiation step, so the specific term GO:2000142 regulation of DNA-templated transcription initiation, which the gene already carries (IEA, GO_REF:0000108), is the right gene-level term. The node-level claim itself is sound and needs no change upstream. Propagation Review Root cause: NO FAILURE CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN002455017 Β· PTN002455017 SUPPORTS TRANSFER ECF sigma factor clade node (250 leaves, 29 taxa; 8 seeds: E. coli RpoE, V. cholerae RpoE, M. tuberculosis SigC/SigH/SigL/SigM, AlgU and PvdS). The node term is appropriate for the clade and the target is a bona fide member; only the granularity for this gene differs. Proposed replacements: regulation of DNA-templated transcription initiation Supporting Evidence: PMID:19730690 Sigma factors are essential subunits of prokaryotic RNA polymerase, they are involved in promoter recognition and transcription initiation file:PSEAE/fpvI/fpvI-uniprot.txt TIGR02937; sigma70-ECF |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | MODIFY | Summary: InterPro sigma-70 domain mapping to regulation of transcription. Reason: Correct but general; refined to the initiation-specific term the gene already carries, consistent with the IBA row. Proposed replacements: regulation of DNA-templated transcription initiation Supporting Evidence: file:PSEAE/fpvI/fpvI-uniprot.txt PF04542; Sigma70_r2 |
| GO:0016987 sigma factor activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the PAINT IBD on PTN002455017, the ECF sigma factor clade of PTHR43133 (16 seeds). fpvI is a member of the clade, with the ECF sigma-70 domain architecture, and is itself one of the seeds, so its own appearance in WITH/FROM is expected, not circular. Reason: Core function. The IBD is well founded on several experimentally characterised ECF sigma factors (E. coli FecI, M. tuberculosis ECF sigmas, PvdS, AlgU with in vitro transcription evidence) and the target retains the sigma-70 region 4.2 module and ECF family membership. Supporting Evidence: file:PSEAE/fpvI/fpvI-uniprot.txt TIGR02937; sigma70-ECF file:PSEAE/fpvI/fpvI-uniprot.txt PF04542; Sigma70_r2 PMID:29729420 the iron starvation Ο (PvdS, FpvI, HasI, FecI, FecI2 and others), the cell wall stress ECFΟ AlgU, SigX and SbrI, and the unorthodox ΟVreI involved in the expression of virulence |
| GO:0016987 sigma factor activity | IDA PMID:12492864 Siderophore-mediated cell signalling in Pseudomonas aerugino... | ACCEPT | Summary: PseudoCAP seed (IDA and IMP rows from this paper). FpvI is required for FpvA synthesis and its activity is controlled by FpvR and induced by ferri-pyoverdine. Reason: Seed verdict SOUND: the paper supports sigma factor activity for this gene, and the term is the core molecular function. Supporting Evidence: PMID:12492864 FpvR negatively regulates the activity of a second ECF sigma factor, FpvI, which is required for the synthesis of FpvA |
| GO:0016987 sigma factor activity | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro sigma-70 region 4 type 2 mapping to sigma factor activity. Reason: Same claim as the IBA and experimental rows, reached from domain signatures; core function. Supporting Evidence: file:PSEAE/fpvI/fpvI-uniprot.txt PF04542; Sigma70_r2 file:PSEAE/fpvI/fpvI-uniprot.txt TIGR02937; sigma70-ECF |
| GO:0016987 sigma factor activity | IMP PMID:12492864 Siderophore-mediated cell signalling in Pseudomonas aerugino... | ACCEPT | Summary: PseudoCAP seed (IDA and IMP rows from this paper). FpvI is required for FpvA synthesis and its activity is controlled by FpvR and induced by ferri-pyoverdine. Reason: Seed verdict SOUND: the paper supports sigma factor activity for this gene, and the term is the core molecular function. Supporting Evidence: PMID:12492864 FpvR negatively regulates the activity of a second ECF sigma factor, FpvI, which is required for the synthesis of FpvA |
| GO:0016987 sigma factor activity | IMP PMID:12562796 Pyoverdine-mediated regulation of FpvA synthesis in Pseudomo... | ACCEPT | Summary: PseudoCAP IMP and seed. Deleting fpvI abolishes pyoverdine-dependent fpvA expression, and cloned fpvI stimulates it: genetic evidence for a promoter-specific sigma factor. Reason: Seed verdict SOUND: the paper supports sigma factor activity for this gene, and the term is the core molecular function. Supporting Evidence: PMID:12562796 Deletion of this gene, dubbed fpvI, compromised pyoverdine-dependent FpvA ferric pyoverdine receptor production and fpvA gene expression, while the cloned gene stimulated fpvA expression |
| GO:2000142 regulation of DNA-templated transcription initiation | IEA GO_REF:0000108 | ACCEPT | Summary: Inferred from sigma factor activity by inter-ontology link; the regulatory process a sigma factor performs. Reason: Correct granularity for the process side of sigma factor activity; replacement target for the GO:0006355 rows. Supporting Evidence: PMID:19730690 Sigma factors are essential subunits of prokaryotic RNA polymerase, they are involved in promoter recognition and transcription initiation file:PSEAE/fpvI/fpvI-uniprot.txt PF04542; Sigma70_r2 |
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Experiment: Purify FpvI and test core RNAP binding and in vitro transcription from the fpvA promoter; map the FpvI promoter element.
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