| Aspect | Key finding | Evidence type | Quantitative/statistical details (if any) | Source (first author year, journal) | URL | Publication date (month year if known) |
|---|---|---|---|---|---|---|
| identity/function | RpoS is the conserved general-stress/stationary-phase alternative sigma factor in many γ-proteobacteria; as a group 2 sigma factor, it binds core RNAP and recognizes promoters similar to RpoD, using σ2/σ3/σ4 domains to engage promoter elements. This supports annotation of PP_1623/Q88ME8 as sigma S rather than an enzyme or transporter. (pqac-00000010, pqac-00000015) | Authoritative review; domain/promoter synthesis | Review notes >300 promoters in the *E. coli* RpoS regulon; emphasizes promoter similarity to σ70/RpoD promoters rather than a catalytic reaction. (pqac-00000010) | Bouillet 2024, *Microbiology and Molecular Biology Reviews* | https://doi.org/10.1128/mmbr.00151-22 | March 2024 |
| regulation/process | In *P. putida* KT2440, RsmA directly binds the untranslated region of **rpoS** mRNA (including the ribosome-binding/start-codon region), supporting post-transcriptional control of RpoS. Through RpoS, the Gac/Rsm cascade connects to **lapF** expression and indirectly to **cfcR**-dependent c-di-GMP signaling. (pqac-00000012, pqac-00000003) | EMSA; RNA target capture; regulatory model | EMSA confirmed RsmA–rpoS RNA binding; **cfcR** transcript showed RsmA enrichment values **1.82** and **1.88** (below cut-off), consistent with modest in vivo enrichment despite prior interaction evidence. (pqac-00000012) | Huertas-Rosales 2021, *Frontiers in Molecular Biosciences* | https://doi.org/10.3389/fmolb.2021.624061 | February 2021 |
| regulation/phenotype | Loss of (p)ppGpp synthesis alters RpoS-linked biofilm regulation in KT2440: ΔrelA and especially ΔrelAΔspoT show reduced **rpoS** promoter activity, increased **lapA**, decreased **lapF**, reduced **pea**, and abnormal pellicle/biofilm architecture. This places RpoS downstream of the stringent response in biofilm control. (pqac-00000013, pqac-00000004, pqac-00000006, pqac-00000007) | Reporter assays (rpoS::lacZ, lapA::lacZ, lapF::lacZ); qRT-PCR; crystal violet biofilm assay; morphology assays | **pea** reduced **2.3-fold** in ΔrelA and **5.8-fold** in ΔRS; **peb** and **bcs** increased about **2.0-fold** and **2.2-fold** in ΔRS; ΔRS showed noticeably increased microtiter biofilm at **22 h** and maintained thick biofilm at **34 h**, while WT dispersed by 34 h. (pqac-00000013) | Liu 2017, *Microbiological Research* | https://doi.org/10.1016/j.micres.2017.07.003 | November 2017 |
| process/phenotype | ArgR links arginine metabolism to c-di-GMP signaling and likely modulates **LapF**, **Pea**, and the diguanylate cyclase **CfcR** through RpoS in KT2440; argR deletion increases biofilm formation and reduces surface motility. (pqac-00000011, pqac-00000005) | Primary genetics/phenotyping study | The excerpt reports qualitative phenotypes (increased biofilm, reduced surface motility) but no explicit fold-change for RpoS-dependent outputs in the provided text. (pqac-00000011) | Barrientos-Moreno 2022, *Applied and Environmental Microbiology* | https://doi.org/10.1128/aem.00064-22 | April 2022 |
| process/application | Arginine acts as an environmental/metabolic cue that raises c-di-GMP in KT2440; the response is associated with altered expression of **RpoS-controlled elements** (**lapF, pea, cfcR**) in arginine-biosynthesis mutants, linking metabolism to RpoS-regulated biofilm output. (pqac-00000014, pqac-00000008) | c-di-GMP biosensor study; biofilm assay; mutant analysis | Biofilm quantified after **10 h** as crystal-violet **A595/OD660**; values were averages from **2 independent experiments** with **4 technical replicates** each; significance by Student’s *t* test (**\*p ≤ 0.05; \*\*p ≤ 0.01**). (pqac-00000014) | Barrientos-Moreno 2020, *Scientific Reports* | https://doi.org/10.1038/s41598-020-70675-x | August 2020 |
| process/regulation | Stationary-phase induction in KT2440 does not necessarily imply positive RpoS control: the K1-T6SS is induced in stationary phase, but transcription is **not dependent on RpoS** and is instead **indirectly repressed by RpoS**. This helps define boundaries of the RpoS regulon. (pqac-00000009, pqac-00000000) | Promoter mapping; mutant regulatory analysis | Four K1-T6SS promoters showed typical **σ70-dependent** features; no fold-change values were given in the provided excerpt for RpoS effects. (pqac-00000009) | Bernal 2023, *Microbiology* | https://doi.org/10.1099/mic.0.001295 | January 2023 |


*Table: This table summarizes the most relevant literature-backed findings for *Pseudomonas putida* KT2440 rpoS (PP_1623), spanning core molecular function, regulation, and organism-specific phenotypes. It highlights where evidence is direct for KT2440 and where recent reviews provide conserved mechanistic context for sigma S.*