| Annotation topic | Key findings | Evidence/citations |
|---|---|---|
| Identity | • Target matches UniProt Q88C75 = TonB family protein encoded by **tonB / PP_5308** in *Pseudomonas putida* KT2440 • Gene symbol **tonB** is common across bacteria, so organism/ortholog verification is essential • Direct PP_5308 experiments are limited; strongest locus-specific support comes from KT2440 genome context plus close *P. putida* relative DOT-T1E with BLAST-supported single-copy homologous cluster in KT2440 | (pqac-00000000, pqac-00000007) |
| Localization | • TonB systems are **inner-membrane/periplasm-spanning energy transducers** rather than outer-membrane transporters • TonB has an N-terminal transmembrane anchor and a periplasmic C-terminal domain that contacts TonB-dependent outer-membrane receptors • ExbB/ExbD form the inner-membrane motor complex that energizes TonB from the proton motive force | (pqac-00000003, pqac-00000004, pqac-00000006) |
| Mechanism | • TonB couples **pmf-derived energy** from ExbB/ExbD to TonB-dependent transporters (TBDTs) • TonB binds receptor **TonB boxes**, promoting plug rearrangement/opening and nutrient passage into the periplasm • General stoichiometry/mechanistic model from recent work: **ExbB pentamer + ExbD dimer** enclosing/engaging TonB | (pqac-00000004, pqac-00000006) |
| Operon / genetic context | • In *P. putida* DOT-T1E, **exbB-exbD-tonB** are tightly linked with only **3 bp** between **exbB** and **exbD** and an **overlap between exbD and tonB** • RT-PCR showed **co-transcription** of **exbB-exbD** and **exbD-tonB** • BLAST analysis indicated the cluster is present as a **single copy in KT2440**, supporting annotation of PP_5308 as the KT2440 TonB ortholog • Figure evidence for operon organization is available | (pqac-00000000, pqac-00000008) |
| Regulated processes / biological role | • KT2440 devotes major capacity to **iron scavenging**, including pyoverdine systems and **29 predicted TonB-dependent receptors** • Thus PP_5308 most plausibly functions in energizing uptake of **siderophores/iron-associated substrates** and possibly other scarce large nutrients • In pseudomonads, TonB-like systems can also influence envelope physiology and receptor-dependent processes beyond classical iron uptake | (pqac-00000005, pqac-00000007) |
| Mutant phenotypes / quantitative data | • In DOT-T1E, an **exbD insertion in the exbBD-tonB operon** increased sensitivity to solvents, antibiotics, and iron limitation • Wild type tolerated **1% (vol/vol) toluene** and **17 g/L 4HBA**, whereas mutant growth was prevented at **6 g/L 4HBA** and it failed sudden toluene shock • Mutant accumulated about **200 nmol [14C]4HBA/U turbidity/min** versus about **15 nmol** in control; another summary reports ~**20-fold** higher accumulation • Complementation with **exbBD-tonB** restored wild-type traits | (pqac-00000001, pqac-00000000, pqac-00000005) |
| Recent mechanistic developments (2024) | • 2024 review synthesizes structural evidence that TonB-dependent uptake uses a **mechanical force-transduction** model from ExbB/ExbD to receptor plugs • 2024 JBC study identified a conserved **TonB D-box** motif coupling TonB to ExbD, refining the motor-assembly model • 2024 in vivo work further supports **TonB-ExbD transmembrane heterodimers**, PMF-dependent ExbD conformational changes, and cyclic TonB action | (pqac-00000002, pqac-00000003, pqac-00000004) |
| Applications | • Functional annotation supports interpreting PP_5308 in **iron acquisition**, rhizosphere fitness, and environmental adaptation of KT2440 • TonB systems are attractive **antimicrobial/drug-delivery targets** because many outer-membrane uptake pathways depend on TonB energization • For KT2440 biotechnology, TonB-linked receptor networks may affect uptake of metals/nutrients relevant to **bioprocessing and environmental performance**, though direct PP_5308 application studies remain sparse | (pqac-00000004, pqac-00000007) |


*Table: This table summarizes the most defensible functional annotation for *Pseudomonas putida* KT2440 TonB (PP_5308/Q88C75), separating direct KT2440 evidence from inference based on TonB-family mechanism and closely related *P. putida* DOT-T1E data. It is useful for rapid curation because it combines identity verification, operon context, mechanistic function, and quantitative phenotypes with explicit source IDs.*