| Claim/Topic | Key details (include quantitative values) | Organism context | Evidence type | Primary source with publication year | URL/DOI | Citation ID |
|---|---|---|---|---|---|---|
| Gene identity of target oprD / PP_1206 | PP1206 is explicitly annotated as **“oprD – basic amino acid specific porin OprD”**; included among CbrB regulon targets with **ChIP-seq enrichment 3.45** | *Pseudomonas putida* KT2442/KT2440 background | ChIP-seq annotation / regulon mapping | Barroso et al., 2018 | https://doi.org/10.1371/journal.pone.0209191 | (pqac-00000029, pqac-00000030) |
| Direct binding of regulator CbrB to oprD promoter | EMSA showed a mobility shift for the **PP1206 (oprD) promoter** with increasing **CbrB concentrations 0, 0.5, 1, 2 μM**, supporting direct promoter binding | *P. putida* KT2442 | EMSA | Barroso et al., 2018 | https://doi.org/10.1371/journal.pone.0209191 | (pqac-00000028, pqac-00000032, pqac-00000033) |
| Regulatory direction of oprD by CbrB | RT-qPCR validation reported **fold change 0.3** for PP1206 when calculated as **KT2442 / ΔcbrB (MPO401)**, with expression values **1.71 ± 0.85** vs **5.77 ± 1.64**; indicates oprD was among targets validated as **repressed** under tested conditions | *P. putida* KT2442 grown in minimal medium with oxaloacetate | RT-qPCR | Barroso et al., 2018 | https://doi.org/10.1371/journal.pone.0209191 | (pqac-00000029, pqac-00000031, pqac-00000034) |
| Condition-dependent induction of PP_1206/OprD | OprD (**PP_1206**) was **exclusively induced under dual carbon+nitrogen limitation**; paper identifies it as a **specific porin implicated in uptake of basic amino acids** | *P. putida* KT2442 chemostats under nutrient limitation | Proteomics / integrated omics | Poblete-Castro et al., 2012 | https://doi.org/10.1186/1475-2859-11-34 | (pqac-00000021) |
| Functional annotation in P. putida omics literature | Nutrient-limitation study links outer membrane remodeling to transporter modulation and specifically notes that OprD facilitates diffusion of **basic amino acids** across the membrane | *P. putida* KT2442 | Omics interpretation / functional annotation | Poblete-Castro et al., 2012 | https://doi.org/10.1186/1475-2859-11-34 | (pqac-00000021) |
| Family-level definition of OprD/Occ porins | OprD-family proteins were redefined as **Occ (outer membrane carboxylate) channels** because efficient substrates generally require a **carboxyl group**; family divided into **OccD** and **OccK** subfamilies | Primarily *P. aeruginosa* family model, relevant by homology to PP_1206 | Structural/functional primary study | Eren et al., 2012 | https://doi.org/10.1371/journal.pbio.1001242 | (pqac-00000002) |
| Archetypal function of OccD1/OprD | **OccD1 (formerly OprD)** is the archetype of the family and is thought to transport **basic amino acids** while also serving as an entry portal for **carbapenem β-lactams** | *P. aeruginosa* family model; used for inference to *P. putida* OprD family membership | Structural/functional primary study | Eren et al., 2012 | https://doi.org/10.1371/journal.pbio.1001242 | (pqac-00000002) |
| Structural determinants of specificity | Occ channels are monomeric β-barrels with a constriction formed by loops **L3 and L7**; conserved **basic ladder** helps define specificity | OprD/Occ family (Pseudomonas) | Structural biology / electrophysiology | Eren et al., 2012 | https://doi.org/10.1371/journal.pbio.1001242 | (pqac-00000009, pqac-00000026) |
| Quantitative channel behavior | Electrophysiology found very small dominant conductances for **OccD1/OccD2 (~15 pS)**, while **OccD3** could show much larger states **(~700 pS)**, highlighting dynamic pore behavior | OprD/Occ family in *P. aeruginosa* | Single-channel electrophysiology | Eren et al., 2012 | https://doi.org/10.1371/journal.pbio.1001242 | (pqac-00000009) |
| Transport assay evidence for substrate bias | Proteoliposome/vesicle uptake assays showed **OccK** channels transport carboxylate-containing substrates well (e.g., glucuronate), whereas **OccD1 arginine uptake was low but above background (>5-fold)**; supports highly selective, difficult-to-measure transport | OprD/Occ family in *P. aeruginosa* | Transport assays | Eren et al., 2012 | https://doi.org/10.1371/journal.pbio.1001242 | (pqac-00000009) |
| Expert synthesis on subfamily functions | Review states the family contains **19 members** in *P. aeruginosa*, split into **8 OccD** and **11 OccK**; **OccD** members are linked to uptake of **basic amino acids**, **OccK** to negatively charged cyclic molecules; channels typically pass small molecules **≤ ~200 Da** | Pseudomonas OprD/Occ family | Authoritative review | Chevalier et al., 2017 | https://doi.org/10.1093/femsre/fux020 | (pqac-00000007) |
| Porin context in Pseudomonas envelope biology | The review emphasizes very low outer-membrane permeability in *Pseudomonas* (**~8% of *E. coli***), explaining why substrate-specific porins like OprD/Occ are physiologically important | *P. aeruginosa* / genus-level context | Authoritative review | Chevalier et al., 2017 | https://doi.org/10.1093/femsre/fux020 | (pqac-00000007) |
| Physiological role of OprD-like subfamily | OprD-subgroup porins take up **amino acids and related molecules such as dipeptides**, whereas OpdK-like porins take up diverse **carboxylic acids**; expression is often **positively regulated by substrates** | *P. aeruginosa* OprD family; useful family-level inference for PP_1206 | Primary genetics/physiology study | Tamber et al., 2006 | https://doi.org/10.1128/JB.188.1.45-54.2006 | (pqac-00000005) |
| Species repertoire context | Comparative analysis reported that *P. putida* harbors more **OpdK-like than OprD-like porins (13 vs 8)**, implying a broad specialized outer-membrane uptake network | *P. putida* species-level context | Comparative phylogeny / thesis synthesis | Tamber, 2010 | https://doi.org/10.14288/1.0093018 | (pqac-00000001) |
| Evidence for carbapenem link and porin redundancy | In a Δ40 porin background, reduced susceptibility to **meropenem and imipenem** could be attributed primarily to **OprD/OccD1**; other porins such as **OpdP/OccD3** may contribute under some conditions | *P. aeruginosa* | Functional physiology | Ude et al., 2021 | https://doi.org/10.1073/pnas.2107644118 | (pqac-00000008) |
| 2024 update on clinical/biophysical significance | Study of **20** strains/isolates found **all 20 induced blaAmpC** after sublethal imipenem exposure and **18 lacked detectable OprD**, supporting that OprD is important but **not the only** route for carbapenem entry; reported imipenem/relebactam MICs **4–256 μg/mL** | *P. aeruginosa* clinical/lab isolates | 2024 primary study | Freed & Hanson, 2024 | https://doi.org/10.1128/spectrum.00142-24 | (pqac-00000010) |
| 2024 expert opinion on regulation and applications | Review highlights **downregulation of influx porins** and **upregulation of efflux pumps** as core inducible resistance mechanisms, and discusses therapeutic strategies that modulate porin/efflux expression to restore susceptibility | *P. aeruginosa* | 2024 review / expert analysis | Wu et al., 2024 | https://doi.org/10.1111/1751-7915.14487 | (pqac-00000014) |


*Table: This table compiles organism-specific evidence for Pseudomonas putida PP_1206/oprD together with authoritative family-level evidence for OprD/OccD porins. It highlights gene identity, regulation, likely substrate specificity, structural basis, and recent 2024 findings relevant to real-world applications such as antibiotic permeability and resistance.*