RpoS (sigma S, PA3622) is the stationary-phase and general stress response sigma factor of Pseudomonas aeruginosa, a group 2 member of the sigma-70 family with conserved regions 1-4 and a C-terminal helix-turn-helix that recognises the -35 element. Bound to core RNA polymerase it directs transcription initiation from RpoS-dependent promoters, such as the psl exopolysaccharide operon and the cheY2-cheA2-cheW2-aer-2 aerotaxis operon. rpoS mutants are hypersensitive to heat, high osmolarity and prolonged peroxide, make less catalase, exotoxin A and alginate, overproduce pyocyanin and pyoverdine, and show altered twitching, aerotaxis and biofilm formation. RpoS availability is controlled post-translationally by the anti-sigma factor domain of HsbR in the HptB-HsbR-HsbA partner switch and by RssB/RssC-dependent ClpXP proteolysis.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000976 transcription cis-regulatory region binding | IBA GO_REF:0000033 | MODIFY | Summary: IBA from PTN000779307 seeded by Arabidopsis SIG3 (TAIR IPI). Reason: Correct but general: a sigma factor, as part of the holoenzyme, recognises the -10 and -35 core promoter elements, so GO:0001046 core promoter sequence-specific DNA binding (is_a GO:0000976) is the precise term, as in the algU and pvdS reviews. The psl promoter carries an RpoS-type -10 element. Propagation Review Root cause: NO FAILURE CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000779307 Β· PTN000779307 SUPPORTS TRANSFER Sound node-level claim for sigma-70 family members; refined at the gene level only. AGI_LocusCode:AT3G53920 Β· Arabidopsis SIG3 (sole seed) SUPPORTS TRANSFER TAIR IPI PMID:25533953 (QuickGO 2026-11-05). Proposed replacements: core promoter sequence-specific DNA binding Supporting Evidence: file:PSEAE/rpoS/rpoS-uniprot.txt Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. file:PSEAE/rpoS/rpoS-uniprot.txt FT DNA_BIND 293..312 FT /note="H-T-H motif" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00959" |
| GO:0003677 DNA binding | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: InterPro/UniRule DNA binding. 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. Supporting Evidence: file:PSEAE/rpoS/rpoS-uniprot.txt FT DNA_BIND 293..312 FT /note="H-T-H motif" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00959" |
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro sigma-70 domain mapping. Reason: True but uninformative; GO:0016987 sigma factor activity, accepted here, is_a GO:0003700. |
| GO:0003899 DNA-directed RNA polymerase activity | IBA GO_REF:0000033 | REMOVE | Summary: IBA from a PTN000779307 IBD seeded only by Arabidopsis SIG3 (TAIR IMP/ISS rows). Reason: A sigma factor has no catalytic site; RNA polymerisation is catalysed by the core enzyme (beta and beta' subunits). RpoS is an initiation specificity factor whose activity is GO:0016987, accepted here. The seed's annotation conflates the sigma subunit with the holoenzyme, and the error propagates to every sigma-70 leaf under the node. Propagation Review Root cause: SOURCE BAD Failure modes: ROLE CONFLATION COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN000779307 Β· PTN000779307 SOURCE BAD Single-seed IBD of a catalytic activity on a sigma-factor clade. AGI_LocusCode:AT3G53920 Β· Arabidopsis SIG3 (sole seed) SOURCE BAD TAIR GO:0003899 IMP PMID:17175536 and ISS PMID:9280303 (QuickGO 2026-11-05); a sigma factor is at most contributes_to the holoenzyme activity. Supporting Evidence: file:PSEAE/rpoS/rpoS-uniprot.txt Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. file:PSEAE/rpoS/rpoS-uniprot.txt Interacts with the RNA polymerase core enzyme. |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: HAMAP subcellular location mapping. Reason: A soluble RNA polymerase subunit; cytoplasm is as precise as warranted for a bacterium. Supporting Evidence: file:PSEAE/rpoS/rpoS-uniprot.txt Interacts with the RNA polymerase core enzyme. |
| GO:0006352 DNA-templated transcription initiation | IEA GO_REF:0000120 | ACCEPT | Summary: InterPro/UniRule sigma-70 mapping. Reason: Sigma factors take part directly in promoter recognition and open-complex formation. Supporting Evidence: file:PSEAE/rpoS/rpoS-uniprot.txt Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. |
| GO:0006355 regulation of DNA-templated transcription | IBA GO_REF:0000033 | TOO GENERAL | Summary: IBA from the 7-seed PTN000779307 IBD; RpoS appears among its sources because of its own PseudoCAP row, which is expected. Reason: True, but GO:2000142 regulation of DNA-templated transcription initiation, accepted here, is_a GO:0006355. The node-level claim is sound and stands on E. coli RpoD and M. tuberculosis SigA without the RpoS seed. |
| GO:0006355 regulation of DNA-templated transcription | IDA PMID:10383954 Effect of rpoS mutation on the stress response and expressio... | TOO GENERAL | Summary: PseudoCAP IDA and one of 7 seeds of PTN000779307. The full text reports rpoS mutant phenotypes only; no transcription was measured. Reason: Seed verdict INDIRECT-PHENOTYPE. The claim is true of a sigma factor and is supported directly elsewhere (psl transcription, PMID:20735777), but this paper shows only phenotypes of an rpoS mutant, which is IMP at most (see source_defects). The term itself is entailed by GO:2000142, accepted here. |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000120 | TOO GENERAL | Summary: InterPro/ARBA mapping. Reason: Entailed by GO:2000142, accepted here; consistent with the IBA and IDA rows. |
| GO:0010468 regulation of gene expression | IEA GO_REF:0000104 | TOO GENERAL | Summary: UniRule mapping to a very general process. Reason: Entailed by GO:2000142 regulation of DNA-templated transcription initiation, accepted here. |
| GO:0016987 sigma factor activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN000779307 seeded by E. coli RpoD and RpoS, M. tuberculosis SigA/SigB, B. subtilis and plant sigma factors. Reason: Core activity; RpoS is a sigma-70 family group 2 sigma factor (HAMAP MF_00959). Supporting Evidence: file:PSEAE/rpoS/rpoS-uniprot.txt HAMAP; MF_00959; Sigma70_RpoS; 1. PMID:20735777 we demonstrate that the alternative Ο-factor RpoS is a positive transcriptional regulator of psl gene expression |
| GO:0016987 sigma factor activity | IEA GO_REF:0000120 | ACCEPT | Summary: InterPro/UniRule mapping. Reason: Same claim as the IBA row. Supporting Evidence: file:PSEAE/rpoS/rpoS-uniprot.txt TIGR02394; rpoS_proteo |
| GO:0050921 positive regulation of chemotaxis | IMP PMID:15687221 Expression of Pseudomonas aeruginosa aer-2, one of two aerot... | KEEP AS NON CORE | Summary: PseudoCAP IMP. RpoS is needed for Aer-2-mediated aerotaxis and expression of the aer-2 operon. Reason: A regulon output of RpoS (transcription of the che2/aer-2 operon), not a core function. Supporting Evidence: PMID:15687221 A deletion-insertion mutation of alternative sigma factor RpoS eliminated Aer-2-mediated aerotaxis but not Aer-mediated aerotaxis. |
| GO:1900034 regulation of cellular response to heat | IMP PMID:10383954 Effect of rpoS mutation on the stress response and expressio... | KEEP AS NON CORE | Summary: PseudoCAP IMP. The rpoS mutant is hypersensitive to 50 Β°C heat shock. Reason: General stress response output of the RpoS regulon. Supporting Evidence: PMID:10383954 In addition, the PAO1 rpoS mutant was hypersensitive to heat shock at 50Β°C, increased osmolarity, and prolonged exposure to high concentrations of H 2 O 2 . |
| GO:1900233 positive regulation of single-species biofilm formation on inanimate substrate | IMP PMID:20735777 Pseudomonas aeruginosa biofilm matrix polysaccharide Psl is ... | KEEP AS NON CORE | Summary: PseudoCAP IMP. RpoS activates psl transcription and the rpoS mutant makes less Psl. Reason: Supported (and the psl regulation is direct), but biofilm formation is one regulon output among many; kept as non-core as for algU. Supporting Evidence: PMID:20735777 we demonstrate that the alternative Ο-factor RpoS is a positive transcriptional regulator of psl gene expression |
| GO:1900377 negative regulation of secondary metabolite biosynthetic process | IMP PMID:10383954 Effect of rpoS mutation on the stress response and expressio... | KEEP AS NON CORE | Summary: PseudoCAP IMP. The rpoS mutant overproduces pyocyanin and pyoverdine. Reason: Two different secondary metabolites are affected, so the general term is as precise as this evidence allows; the effect may be indirect (quorum sensing). Supporting Evidence: PMID:10383954 The rpoS mutation resulted in the increased production of the phenazine antibiotic pyocyanin and the siderophore pyoverdine. |
| GO:1900407 regulation of cellular response to oxidative stress | IMP PMID:10383954 Effect of rpoS mutation on the stress response and expressio... | KEEP AS NON CORE | Summary: PseudoCAP IMP. H2O2 hypersensitivity and 60% less catalase in the rpoS mutant. Reason: General stress response output of the RpoS regulon. Supporting Evidence: PMID:10383954 In accordance with the hypersensitivity to H 2 O 2 , catalase production was 60% lower in the rpoS mutant than in the parent strain. |
| GO:1901000 regulation of response to salt stress | IMP PMID:10383954 Effect of rpoS mutation on the stress response and expressio... | KEEP AS NON CORE | Summary: PseudoCAP IMP. The rpoS mutant is hypersensitive to increased osmolarity. Reason: General stress response output of the RpoS regulon. Supporting Evidence: PMID:10383954 In addition, the PAO1 rpoS mutant was hypersensitive to heat shock at 50Β°C, increased osmolarity, and prolonged exposure to high concentrations of H 2 O 2 . |
| GO:1903865 sigma factor antagonist complex | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA from PTN000779307 seeded by E. coli RpoD and RpoS (ComplexPortal IPI rows). In P. aeruginosa RpoS binds the anti-sigma factor domain of HsbR. Reason: Gene-specific evidence (bacterial two-hybrid) supports an RpoS-HsbR anti-sigma complex. The complex is regulatory, not where RpoS acts, so it is kept as non-core. Supporting Evidence: PMID:31019225 Clearly, HsbRD3 interacted with RpoS from P. aeruginosa as well as with CrsR. PMID:31019225 We established that HsbR is an anti-sigma factor controlling RpoS and unveiled a connection between the HptB-HsbR-HsbA signal transduction cascade and the RpoS pathway during biofilm biogenesis. |
| GO:2000142 regulation of DNA-templated transcription initiation | IEA GO_REF:0000108 | ACCEPT | Summary: Logical inference from sigma factor activity. Reason: A sigma factor regulates transcription at the initiation step. Supporting Evidence: PMID:20735777 we demonstrate that the alternative Ο-factor RpoS is a positive transcriptional regulator of psl gene expression |
| GO:2000145 regulation of cell motility | IMP PMID:10383954 Effect of rpoS mutation on the stress response and expressio... | KEEP AS NON CORE | Summary: PseudoCAP IMP. The rpoS mutant has an altered twitching phenotype. Reason: Twitching is affected without a stated sign, so the unsigned general term fits; a regulon output. Supporting Evidence: PMID:10383954 In addition, the rpoS mutant displayed an altered twitching-motility phenotype, suggesting that the colonization factors, type IV fimbriae, were affected. |
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Experiment: Reconstitute RpoS-holoenzyme transcription in vitro on the psl and aer-2 promoters, with and without the HsbR anti-sigma domain and phosphorylated HsbA.
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