VreI (PA0675) is a 181-residue extracytoplasmic function (ECF) sigma factor of Pseudomonas aeruginosa PAO1. It is the sigma component of the PUMA3 cell-surface signalling system, with the periplasmic receptor-like protein VreA (PA0674) and the inner-membrane sigma factor regulator VreR (PA0676). VreR both holds VreI at the membrane and is required for its activity. When VreI is overexpressed it induces about 27 genes, mostly downstream of the PUMA3 locus. These include the Hxc type II secretion system and its substrate alkaline phosphatase, a two-partner secretion system and exbBD homologues. PUMA3 induction increases virulence in a zebrafish embryo infection model. VreI carries a sigma-70 region 4.2 helix-turn-helix; its region 2 is divergent and not detected by the Pfam Sigma70_r2 model, though the sigma region 2 superfamily signature is present.
| 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/vreI/vreI-uniprot.txt PF08281; Sigma70_r4_2 |
| 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/vreI/vreI-uniprot.txt PF08281; Sigma70_r4_2 |
| GO:0005829 cytosol | NAS PMID:19730690 A Novel extracytoplasmic function (ECF) sigma factor regulat... | 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 VreI is associated to the membrane through the VreR sigma factor regulator |
| 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/vreI/vreI-uniprot.txt PF08281; Sigma70_r4_2 |
| 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 vreI 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/vreI/vreI-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/vreI/vreI-uniprot.txt PF08281; Sigma70_r4_2 |
| 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). vreI 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/vreI/vreI-uniprot.txt TIGR02937; sigma70-ECF file:PSEAE/vreI/vreI-uniprot.txt PF08281; Sigma70_r4_2 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/vreI/vreI-uniprot.txt PF08281; Sigma70_r4_2 file:PSEAE/vreI/vreI-uniprot.txt TIGR02937; sigma70-ECF |
| GO:0016987 sigma factor activity | IMP PMID:19730690 A Novel extracytoplasmic function (ECF) sigma factor regulat... | ACCEPT | Summary: PseudoCAP IMP and seed of the PTN002455017 IBD. Overexpressed VreI induced ~27 target genes, an induction that needs the regulator VreR. The evidence is genetic: no RNAP binding or in vitro transcription. Reason: Seed verdict SOUND: the paper supports sigma factor activity for this gene, and the term is the core molecular function. Supporting Evidence: PMID:19730690 overexpression of vreI upregulates 30 genes |
| 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/vreI/vreI-uniprot.txt PF08281; Sigma70_r4_2 |
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Download this section (compressed HTML)Q: VreI lacks a Pfam-detectable sigma-70 region 2. Does it still bind core RNA polymerase on its own, or does VreR's positive role reflect a need for a partner to stabilise a holoenzyme?
Experiment: Reconstitute VreI with core RNAP and test promoter binding and in vitro transcription at the hxc and PA0691 promoters.
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