TonB (VPARA_25820) is a 232-amino-acid inner-membrane proton-motive-force energy transducer in Variovorax paradoxus TBEA6 encoded in the conserved exbD5-exbB4-tonB-bfrD1 (VPARA_25800-VPARA_25830) locus immediately upstream of the outer-membrane TonB-dependent ferric-siderophore receptor bfrD1 (VPARA_25830). Anchored in the cytoplasmic membrane by a single N-terminal transmembrane helix (residues 18-35) within the TonB-ExbB-ExbD complex, TonB extends across the periplasmic space via a disordered linker region (residues 58-143) containing two proline-rich compositionally biased segments (residues 59-87 and 95-135) so that its globular C-terminal domain (PROSITE PS52015, Pfam PF03544, residues 140-232) engages the periplasmic TonB box of ligand-loaded outer-membrane TonB-dependent receptors, mechanically coupling the inner-membrane proton gradient to active import of ferric-siderophore complexes across the outer membrane.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Core subcellular localization; TonB is anchored in the bacterial inner (plasma) membrane via its N-terminal transmembrane helix (residues 18-35). Reason: TonB possesses a single N-terminal transmembrane alpha-helix (residues 18-35) that anchors the protein in the cytoplasmic (plasma) membrane and interacts with ExbB and ExbD to harvest the proton-motive force. Supporting Evidence: UniProtKB:A0A0H2M2E3 SUBCELLULAR LOCATION: Cell inner membrane {ECO:0000256|ARBA:ARBA00004383, ECO:0000256|PROSITE-ProRule:PRU01359}; Single-pass membrane protein PMID:20420522 The transport process requires energy in the form of proton motive force and a complex of three inner membrane proteins, TonB-ExbB-ExbD, to transduce this energy to the outer membrane. |
| GO:0015031 protein transport | IEA GO_REF:0000104 | REMOVE | Summary: Automated UniRule over-annotation; TonB transduces energy to outer-membrane receptors for ferric-siderophore and small-molecule nutrient uptake rather than mediating protein translocation. Reason: UniRule UR001806740 propagates GO:0015031 (protein transport) to bacterial TonB proteins, likely reflecting opportunistic exploitation of the TonB system by bacteriophages and colicin protein toxins in enteric bacteria. Physiologically, TonB energizes active outer-membrane import of ferric-siderophore chelates, vitamin B12, and nickel/carbohydrate complexes, and is not a protein translocase. Supporting Evidence: PMID:20420522 TonB-dependent transporters (TBDTs) are bacterial outer membrane proteins that bind and transport ferric chelates, called siderophores, as well as vitamin B(12), nickel complexes, and carbohydrates. |
| GO:0030288 outer membrane-bounded periplasmic space | IEA GO_REF:0000104 | ACCEPT | Summary: Core subcellular compartment spanned by the disordered periplasmic linker region (residues 58-143, containing proline-rich segments at 59-87 and 95-135) and C-terminal receptor-binding domain (residues 140-232) of TonB. Reason: While anchored in the inner membrane at residues 18-35, the bulk of TonB (the disordered linker region at residues 58-143 containing proline-rich segments at residues 59-87 and 95-135, plus the C-terminal globular domain at residues 140-232) resides in and spans the Gram-negative outer membrane-bounded periplasmic space to contact outer-membrane TonB-dependent receptors. Supporting Evidence: UniProtKB:A0A0H2M2E3 Single-pass membrane protein {ECO:0000256|ARBA:ARBA00004383, ECO:0000256|PROSITE-ProRule:PRU01359}; Periplasmic side PMID:20420522 The plug domain functions to bind a specific metal chelate at the extracellular side of the membrane and to interact with TonB-ExbB-ExbD at the periplasmic side of the outer membrane. |
| GO:0031992 energy transducer activity | IEA GO_REF:0000120 | ACCEPT | Summary: Core molecular function of TonB, which transduces the inner-membrane proton-motive force into mechanical work on outer-membrane TonB-dependent receptors. Reason: TonB couples the proton-motive force generated across the cytoplasmic membrane (via ExbB/ExbD) to conformational opening of the plug domain in outer-membrane TonB-dependent receptors via its C-terminal domain (Pfam PF03544, PROSITE PS52015). Supporting Evidence: UniProtKB:A0A0H2M2E3 FT DOMAIN 140..232 FT /note="TonB C-terminal" FT /evidence="ECO:0000259|PROSITE:PS52015" PMID:20420522 The transport process requires energy in the form of proton motive force and a complex of three inner membrane proteins, TonB-ExbB-ExbD, to transduce this energy to the outer membrane. |
| GO:0055085 transmembrane transport | IEA GO_REF:0000120 | MODIFY | Summary: Correct but overly general biological process term; refine to GO:0015891 (siderophore transport) to reflect the role of VPARA_25820 in energizing outer-membrane ferric-siderophore uptake within the exbD5-exbB4-tonB-bfrD1 (VPARA_25800-VPARA_25830) locus. Reason: GO:0055085 (transmembrane transport) is a broad parent term. VPARA_25820 is encoded in the exbD5-exbB4-tonB-bfrD1 (VPARA_25800-VPARA_25830) locus immediately adjacent to the TonB-dependent ferric-siderophore receptor bfrD1 (VPARA_25830) and functions specifically to energize outer-membrane siderophore transport (GO:0015891). Proposed replacements: siderophore transport Supporting Evidence: PMID:20420522 These transporters show high affinity and specificity for metal chelates called siderophores and require energy derived from the protonmotive force across the inner membrane to transport them (33, 87). To tap this energy source, TBDTs must interact with an inner membrane protein complex consisting of TonB, ExbB, and ExbD (72). |
| GO:0098797 plasma membrane protein complex | IEA GO_REF:0000118 | ACCEPT | Summary: Accurate complex localization representing the inner-membrane TonB-ExbB-ExbD energy-transducing complex. Reason: TonB assembles with the integral inner-membrane proteins ExbB (VPARA_25810) and ExbD (VPARA_25800) to form the plasma-membrane TonB-ExbB-ExbD proton-motive-force harvesting complex. Supporting Evidence: PMID:20420522 The transport process requires energy in the form of proton motive force and a complex of three inner membrane proteins, TonB-ExbB-ExbD, to transduce this energy to the outer membrane. |
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Download this section (compressed HTML)Q: Does VPARA_25820 (tonB) specifically energize only the adjacent BfrD1 (VPARA_25830) receptor in Variovorax paradoxus TBEA6, or does it serve as a general energy transducer for multiple outer-membrane TonB-dependent siderophore and metallophore receptors encoded elsewhere in the genome?
Suggested experts: Noinaj N, Postle K, Cornelis P
Experiment: Construct a ΞtonB (VPARA_25820) deletion mutant in Variovorax paradoxus TBEA6 and compare its growth under iron starvation with a ΞbfrD1 (VPARA_25830) mutant in the presence of endogenous variobactin and exogenous xenosiderophores.
Hypothesis: Deletion of VPARA_25820 abolishes BfrD1-dependent ferric-siderophore import and reveals whether parallel TonB homologs in V. paradoxus can partially compensate.
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