Gene Ontology annotation through association of InterPro records with GO terms

Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features

GO_REF:0000108

Automatic assignment of GO terms using logical inference, based on on inter-ontology links

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

PMID:9642197

Cloning, sequencing, and phenotypic characterization of the rpoS gene from Pseudomonas putida KT2440.

PMID:11371535

Regulation of rpoS gene expression in Pseudomonas: involvement of a TetR family regulator.

PMID:11914368

TetR family member psrA directly binds the Pseudomonas rpoS and psrA promoters.

PMID:24488315

Roles of cyclic Di-GMP and the Gac system in transcriptional control of the genes coding for the Pseudomonas putida adhesins LapA and LapF.

PMID:28677348

The Pseudomonas putida CsrA/RsmA homologues negatively affect c-di-GMP pools and biofilm formation through the GGDEF/EAL response regulator CfcR.

PMID:28945818

The promoter region of lapA and its transcriptional regulation by Fis in Pseudomonas putida.

PMID:39589111

Tetracycline induces wsp operon expression to promote biofilm formation in Pseudomonas putida.

file:PSEPK/rpoS/rpoS-notes.md

Curator notes for rpoS in Pseudomonas putida KT2440

RpoS is the stationary-phase sigma factor in KT2440 and its loss impairs starvation survival and starvation-associated cross-protection.

"In KT2440, the rpoS mutant showed reduced survival of carbon starvation and reduced cross-protection against other types of stress in cells starved for carbon, and RpoS controlled expression of more than 50 peptides after short carbon starvation."
PsrA directly activates rpoS transcription and binds the rpoS promoter.

"PsrA binds directly to the rpoS promoter from positions -59 to -35 relative to the transcription start site."
RpoS participates in biofilm-associated pathways through wspA, cfcR, lapA, and lapF regulation.

"RpoS directly bound the major wspA promoter and was required for tetracycline to induce wspA activity and promote biofilm formation."

file:PSEPK/rpoS/rpoS-deep-research-codex.md

Deep research report for rpoS in Pseudomonas putida KT2440

The core GO curation should center on sigma factor activity and transcription initiation rather than generic DNA-binding transcription factor terms.

"Accept GO:0006352 DNA-templated transcription initiation as the direct process executed by RpoS-containing holoenzyme."
Response to starvation is a justified new process annotation from the original KT2440 mutant phenotype.

"Add response to starvation as a justified new BP term supported by the KT2440 mutant phenotype."

file:PSEPK/rpoS/rpoS-uniprot.txt

UniProt entry Q88ME8

Q88ME8 is RNA polymerase sigma factor RpoS, a sigma-70 family RpoS-subfamily protein.

"CC -!- SIMILARITY: Belongs to the sigma-70 factor family. RpoS subfamily."
UniProt describes RpoS as the master transcriptional regulator of the stationary phase and the general stress response, localized to the cytoplasm.

"This sigma factor is the master transcriptional regulator of the stationary phase and the general stress response."

file:PSEPK/rpoS/rpoS-deep-research-falcon.md

Falcon deep research report for rpoS (Q88ME8) in Pseudomonas putida KT2440

RpoS is an alternative sigma-70 family (group 2) sigma factor that binds core RNA polymerase and redirects transcription to promoters supporting survival during stationary phase and the general stress response.

"RpoS is an alternative sigma factor** (sigma-70 family; “group 2” sigma) that binds the **core RNA polymerase** and redirects transcription to a broad set of promoters that support survival during **stationary phase** and diverse stresses—commonly termed the **general stress response (GSR)**"
RpoS does not catalyze a biochemical reaction and is not a transporter; its primary function is sequence-specific transcription initiation control.

"RpoS does **not** catalyze a biochemical reaction and is **not** a transporter. Its primary function is **sequence-specific transcription initiation control**"
As a group 2 sigma factor RpoS binds core RNAP and recognizes promoters similar to RpoD, supporting annotation as sigma S rather than an enzyme or transporter.

"as a group 2 sigma factor, it binds core RNAP and recognizes promoters similar to RpoD"
RpoS competes with the housekeeping sigma RpoD for a limiting pool of core RNA polymerase (sigma competition), framing a growth-versus-survival tradeoff.

"A central concept is **sigma competition**: RpoS competes with the housekeeping sigma **RpoD (σ70)** and other alternative sigmas for a limiting pool of core RNAP."
RpoS is a cytosolic transcription factor that exerts its function by interacting with cytosolic RNA polymerase and promoter DNA.

"RpoS is a **cytosolic** transcription factor (sigma factor) that exerts its function by interacting with **cytosolic RNA polymerase** and promoter DNA."
RpoS-dependent regulons increase tolerance to oxidative, osmotic, temperature, and pH stress and other stationary-phase threats.

"RpoS-dependent regulons typically include genes that increase tolerance to oxidative stress, osmotic stress, temperature and pH extremes, and other stationary-phase threats."
In KT2440, RsmA directly binds the rpoS mRNA ribosome-binding site and start codon (confirmed by EMSA), supporting post-transcriptional control of RpoS levels via the Gac/Rsm network.

"binding of RsmA to an RNA fragment containing the **ribosome-binding site and start codon** of rpoS was confirmed by **EMSA**"
In KT2440, lapF transcription is dependent on RpoS and cfcR expression is regulated by RpoS, embedding RpoS in the c-di-GMP-controlled biofilm circuit.

"lapF transcription is described as dependent on RpoS in KT2440 biofilm literature"
Stationary-phase induction does not always imply RpoS activation; the KT2440 K1-T6SS is induced in stationary phase but is not RpoS-dependent and is indirectly repressed by RpoS, defining a boundary of the RpoS regulon.

"K1-T6SS is induced in stationary phase but is not RpoS-dependent and is indirectly repressed by RpoS"