| Use case | Metric/data (with units) | Experimental context | Interpretation | Source (year) | URL | Citation ID |
|---|---|---|---|---|---|---|
| Housekeeping sigma assignment in native promoter control | **4 σ70-dependent promoters** identified in the K1-T6SS locus | *Pseudomonas putida* KT2440 K1 type VI secretion system transcriptional mapping | Direct evidence that RpoD/σ70 drives multiple native promoters in a biologically relevant competitive system | Bernal et al. (2023) | https://doi.org/10.1099/mic.0.001295 | (pqac-00000014, pqac-00000023) |
| Promoter-reporter implementation | Promoter fragments cloned for functional assays: **343 bp (PtagB1), 507 bp (Phcp1), 456 bp (PvrgG1)**; additional regions **173 bp** and **711 bp** | lacZ reporter fusions and promoter analyses in *P. putida* KT2440 | Real-world implementation of σ70-regulated promoter analysis in KT2440 | Bernal et al. (2023) | https://doi.org/10.1099/mic.0.001295 | (pqac-00000023) |
| Stress physiology readout of rpoD expression | rpoD/PP_0387 RNA-seq values **2845.4 vs 2825.1**, reported **fold-change 1.1 down** | *P. putida* KT2440 relA/spoT mutant, exponential vs stationary phase during mcl-PHA process | Suggests rpoD transcript abundance remained broadly stable across this transition in the tested mutant background | Mozejko-Ciesielska et al. (2017) | https://doi.org/10.1186/s13568-017-0396-z | (pqac-00000013, pqac-00000025) |
| Exponential-growth housekeeping role | Qualitative but functionally specific: rpoD identified as **primary sigma factor during exponential growth** | Desiccation/rehydration transcriptomics in KT2440 | Supports use of rpoD as a marker of growth-associated transcriptional capacity | López-Lara et al. (2020) | https://doi.org/10.1186/s13213-020-01596-3 | (pqac-00000000, pqac-00000018) |
| Reference-gene implementation in RT-qPCR workflows | **30 PCR cycles**; calibration range **1×10^-3 to 1000 ng** plasmid DNA; sampling at **OD650 = 1.5** and **8 h** after inoculation | RT-qPCR in *P. putida* KT2440 biosynthetic-gene expression study using rpoD as internal reference | Shows operational use of rpoD for normalization and transcript-copy correction in applied biotechnology experiments | Domröse et al. (2019) | https://doi.org/10.1038/s41598-019-43405-1 | (pqac-00000022) |
| Reference-gene stability under metal stress | Zinc treatments **0.2, 1.5, 2.5 mmol L^-1**; growth inhibition after 6 h about **5%, 40%, 80%**; RNA-seq libraries **11.3–15.8 million reads/sample** with **83.4% mapping**; **15 genes** validated by RT-qPCR; **3 biological replicates** | Zinc-stress transcriptomics in *P. putida* KT2440; rsd/algQ used as stable internal reference linked to RpoD regulation | Demonstrates the quantitative scale of KT2440 transcriptome studies in which RpoD-associated housekeeping control is important for normalization | Peng et al. (2018) | https://doi.org/10.3389/fmicb.2018.01669 | (pqac-00000004, pqac-00000024) |
| Adaptive evolution / strain engineering | **Ser552Pro** substitution in **rpoD*** (reported in strains PD580/PD689) | 2024 adaptive evolution and metabolic engineering of xylose utilization in KT2440 derivatives | Recent evidence that subtle RpoD variation is selected/used during strain adaptation, underscoring its systems-level importance | Dvořák et al. (2024) | https://doi.org/10.1038/s41467-024-46812-9 | (pqac-00000001, pqac-00000003, pqac-00000016) |
| Closely related Pseudomonas reference-gene validation | rpoD ranked among the most stable reference genes alongside other candidates in comparative validation pipelines | *Pseudomonas brassicacearum* GS20 and prior cited *Pseudomonas* studies | Supports transferability of rpoD as a practical normalization gene across pseudomonads, though condition-specific validation remains necessary | Bai et al. (2020) | https://doi.org/10.1371/journal.pone.0227927 | (pqac-00000005) |


*Table: This table compiles quantitative findings and practical implementations involving rpoD/RpoD(σ70) in Pseudomonas putida KT2440 and related pseudomonads. It is useful for linking functional annotation to measurable experimental evidence and biotechnology use.*