| Claim/Concept | Evidence summary | Organism/Context | Source (authors year journal) | URL | Citation ID |
|---|---|---|---|---|---|
| Verified identity of target protein | UniProt target Q88QU7 matches **rpoD** in *Pseudomonas putida* KT2440; literature excerpts identify **rpoD, PP_0387** as the **RNA polymerase sigma-70 factor/RpoD**. | *P. putida* KT2440 | López-Lara et al. 2020 *Annals of Microbiology*; Benigno et al. unknown journal; Dvořák et al. 2024 *Nature Communications* | https://doi.org/10.1186/s13213-020-01596-3 ; https://doi.org/10.1038/s41467-024-46812-9 | (pqac-00000000, pqac-00000002, pqac-00000003) |
| Primary molecular function | RpoD/σ70 is the **primary/housekeeping sigma factor** that associates with RNAP core to confer promoter specificity and initiate transcription at housekeeping promoters. | General bacterial σ70 framework, applicable to KT2440 annotation | Bouillet et al. 2024 *MMBR*; Busby & Browning 2024 *EcoSal Plus* | https://doi.org/10.1128/mmbr.00151-22 ; https://doi.org/10.1128/ecosalplus.esp-0039-2020 | (pqac-00000007, pqac-00000008, pqac-00000011) |
| Promoter recognition domains | Conserved σ70-family domains mediate promoter recognition: **σ2** recognizes the **-10** element, **σ4** recognizes the **-35** element; domain 3 can recognize extended -10 motifs, and these interactions position RNAP for open-complex formation. | Mechanistic model for bacterial σ70 factors | Busby & Browning 2024 *EcoSal Plus*; Hinton 2025 *EcoSal Plus* | https://doi.org/10.1128/ecosalplus.esp-0039-2020 ; https://doi.org/10.1128/ecosalplus.esp-0006-2025 | (pqac-00000006, pqac-00000007) |
| Structural current understanding | 2024 evidence supports that free σ70 can adopt a **compact apo conformation** and becomes extended upon RNAP binding, exposing DNA-binding surfaces needed for high-affinity promoter recognition and transcription initiation. | Experimental σ70 biophysics; informs interpretation of RpoD function | Joron et al. 2024 *iScience* | https://doi.org/10.1101/2022.10.14.512049 | (pqac-00000009, pqac-00000012) |
| Expression behavior in *P. putida* stress physiology | In desiccated/rehydrated KT2440 cells, **rpoD (PP_0387)** was repressed; authors interpret this as consistent with reduced growth/protein synthesis because RpoD is the primary sigma factor during exponential growth. | *P. putida* KT2440 VBNC/resuscitation study | López-Lara et al. 2020 *Annals of Microbiology* | https://doi.org/10.1186/s13213-020-01596-3 | (pqac-00000000) |
| Expression behavior in stationary-phase transition | In a **relA/spoT** mutant, RNA-seq reported **rpoD/PP_0387** with only ~**1.1-fold down** and no statistically significant change between exponential and stationary phase, indicating stable transcript abundance in that background. | *P. putida* KT2440 relA/spoT mutant during mcl-PHA process | Mozejko-Ciesielska et al. 2017 *AMB Express* | https://doi.org/10.1186/s13568-017-0396-z | (pqac-00000013) |
| σ70 dependence of native promoters in *P. putida* | The K1-T6SS cluster contains **four σ70-dependent promoters**; most T6SS promoters are described as dependent on the housekeeping sigma factor **σ70/RpoD**. | *P. putida* KT2440 K1 type VI secretion system | Bernal et al. 2023 *Microbiology* | https://doi.org/10.1099/mic.0.001295 | (pqac-00000014) |
| Experimental PrpoD reporter use | A **PrpoD (PP_0387)** promoter fragment was cloned into a **lacZ reporter plasmid** and introduced into KT2440/mutants for in vivo promoter assays under light/dark conditions, demonstrating direct experimental use of the native rpoD promoter. | *P. putida* KT2440 promoter-reporter assay | Sumi et al. 2020 *Journal of Bacteriology* | https://doi.org/10.1128/jb.00146-20 | (pqac-00000015) |
| Recent mutation evidence | Recent adaptive-evolution work identified/used **rpoD\*** alleles with **Ser552Pro** substitutions in KT2440 derivatives, explicitly annotating rpoD as encoding RNAP sigma factor **σ70**. | Engineered/evolved *P. putida* xylose-utilizing strains | Dvořák et al. 2024 *Nature Communications* | https://doi.org/10.1038/s41467-024-46812-9 | (pqac-00000001, pqac-00000003, pqac-00000016) |
| Application: RT-qPCR normalization | rpoD is widely used as a **reference/housekeeping gene** in *Pseudomonas* expression studies; in KT2440-related work, stability or prior validation is cited when normalizing RT-qPCR data. | KT2440 stress, chemotaxis, acetate and related studies | Peng et al. 2018 *Frontiers in Microbiology*; Bai et al. 2020 *PLOS ONE* | https://doi.org/10.3389/fmicb.2018.01669 ; https://doi.org/10.1371/journal.pone.0227927 | (pqac-00000004, pqac-00000005) |
| Application: industrial/synthetic-biology relevance | Because KT2440 is a prominent **industrial and synthetic-biology chassis**, understanding RpoD/σ70 is relevant for promoter choice, transcriptional load, pathway expression, and adaptation during strain engineering. | KT2440 biotechnology platform | Dvořák et al. 2024 *Nature Communications*; Loeschcke & Thies 2015 *Applied Microbiology and Biotechnology* | https://doi.org/10.1038/s41467-024-46812-9 ; https://doi.org/10.1007/s00253-015-6745-4 | (pqac-00000001) |


*Table: This table verifies the identity of Q88QU7 as rpoD/PP_0387 in Pseudomonas putida KT2440 and summarizes core functional concepts, organism-specific experimental evidence, and practical applications. It is useful as a compact evidence map for annotation and report writing.*