PA4896 is a 178-residue extracytoplasmic function (ECF) sigma factor of the sigma-70 family (iron-starvation/FecI-like group) in Pseudomonas aeruginosa PAO1. It has the sigma-70 region 2 (core RNA polymerase binding, -10 recognition) and region 4.2 (-35 recognition helix-turn-helix) modules. It forms a cell-surface signalling (CSS) system with the adjacent anti-sigma factor PA4895 and the TonB-dependent transducer PA4897. When overexpressed it induces transcription of the cognate TonB-dependent outer membrane transducer and of putative metal-transport genes, consistent with a role in signal-dependent uptake of an as yet unidentified (probably metal-chelate) substrate. Like other ECF sigma factors it is expected to act in the cytoplasm as the promoter-specificity subunit of RNA polymerase holoenzyme, held inactive by its membrane anti-sigma factor until the signal is perceived.
| 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/PA4896/PA4896-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/PA4896/PA4896-uniprot.txt PF04542; Sigma70_r2 |
| GO:0005829 cytosol | NAS PMID:18086184 Characterization of five novel Pseudomonas aeruginosa cell-s... | ACCEPT | Summary: PseudoCAP NAS cytosol. ECF sigma factors act on RNA polymerase in the cytoplasm; in inducing-off conditions they are held at the inner membrane by their anti-sigma factor. Reason: Location of the active sigma factor and of its holoenzyme; consistent with fractionation data for the family in P. aeruginosa. Supporting Evidence: PMID:19730690 Sigma factors are essential subunits of prokaryotic RNA polymerase, they are involved in promoter recognition and transcription initiation |
| 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/PA4896/PA4896-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 PA4896 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/PA4896/PA4896-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/PA4896/PA4896-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). PA4896 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/PA4896/PA4896-uniprot.txt TIGR02937; sigma70-ECF file:PSEAE/PA4896/PA4896-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 | 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/PA4896/PA4896-uniprot.txt PF04542; Sigma70_r2 file:PSEAE/PA4896/PA4896-uniprot.txt TIGR02937; sigma70-ECF |
| GO:0016987 sigma factor activity | IMP PMID:18086184 Characterization of five novel Pseudomonas aeruginosa cell-s... | ACCEPT | Summary: PseudoCAP IMP and seed of the PTN002455017 IBD. PA4896 overexpression induced its cognate TonB-dependent transducer and putative transport genes. This is genetic evidence that PA4896 directs transcription of specific promoters, the expected readout for an ECF 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:18086184 All five ECF sigma factors control the production of one TonB-dependent transducer |
| GO:0034756 regulation of iron ion transport | IMP PMID:18086184 Characterization of five novel Pseudomonas aeruginosa cell-s... | UNDECIDED | Summary: PseudoCAP IMP regulation of iron ion transport. In the abstract the PA4896 targets are its TonB-dependent transducer and putative (metal) transport systems; no iron-uptake or ligand assay is described for PA4896, and a ligand is named only for FemI (PA1912). Reason: Plausible, since the system resembles siderophore-sensing CSS systems, but the transported substrate of the PA4896 system is unidentified in the abstract and the full text is not accessible. Not removed because the curator may have seen iron-dependent data in the full text. Supporting Evidence: PMID:18086184 although 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; 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/PA4896/PA4896-uniprot.txt PF04542; Sigma70_r2 |
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Experiment: Screen siderophores and metal chelates for induction of a PA4896-dependent lacZ reporter in wild-type versus PA4897 and PA4895 mutants, with in vitro transcription by reconstituted PA4896-RNAP.
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