PvdR (PA2389) is the periplasmic membrane fusion protein (MFP, MacA-like) of the tripartite ATP-binding cassette efflux pump PvdRT-OpmQ, which also contains the inner-membrane ABC transporter PvdT and the outer-membrane channel OpmQ. The pump moves the siderophore pyoverdine from the periplasm to the extracellular medium. It secretes newly made pyoverdine after its periplasmic maturation, recycles pyoverdine released from ferri-pyoverdine after uptake by FpvA, and expels pyoverdine complexed with non-iron metals. Mutants accumulate pyoverdine in the periplasm. The pvdRT-opmQ operon is iron-regulated and depends on the sigma factor PvdS. The pump does not contribute to antibiotic resistance.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0002049 pyoverdine biosynthetic process | IMP PMID:12686626 Identification and characterization of novel pyoverdine synt... | MODIFY | Summary: PseudoCAP IMP from a screen that mutated candidate pvd genes and measured pyoverdine. The mutant phenotype (less extracellular pyoverdine) reflects loss of export and recycling, and the full text of PMID:19906986 attributes the lower yield to reduced synthesis secondary to the export defect. The pump does no step of the biosynthetic chemistry. Not an IBD seed. Reason: Indirect phenotype annotated as participation in biosynthesis. The protein takes part in pyoverdine transport, so the claim is re-pointed to GO:0015891 siderophore transport (PSEUDOCAP WRONG_TERM, PROBABLE). Proposed replacements: siderophore transmembrane transport Supporting Evidence: PMID:19906986 our preliminary results suggest that the lower PVD levels in their culture supernatants are a result of reduced PVD synthesis rather than of impaired secretion of de novo synthesized PVD PMID:19906986 Therefore, the entire PvdRT-OpmQ system (i.e., the IM ABC transporter PvdT, the periplasmic fusion protein PvdR, and the OM porin OpmQ) appears to be involved in the transport of PVD from the periplasm to the extracellular milieu. |
| GO:0015562 efflux transmembrane transporter activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN001253051, the MdtA/PvdR-like MFP clade (87 leaves, 21 taxa). Seeds are PvdR itself (expected self-seed, PseudoCAP IDA/IMP) and Salmonella MdtA (Q8ZNQ3, IDA PMID:24960027, AgBase). The node stands on MdtA alone, and PvdR's own genetics also support it. Reason: The MFP is an obligate part of the PvdRT-OpmQ exporter. GO annotates MFPs of tripartite pumps with the pump's transporter activity; contributes_to would be the more exact qualifier, but the claim is sound. Supporting Evidence: PMID:19906986 Therefore, the entire PvdRT-OpmQ system (i.e., the IM ABC transporter PvdT, the periplasmic fusion protein PvdR, and the OM porin OpmQ) appears to be involved in the transport of PVD from the periplasm to the extracellular milieu. PMID:22187978 PvdRT-OpmQ is an ATP-dependent efflux pump involved in the secretion of newly synthesized pyoverdine (PVD) and of PVD that has transported and released its iron into the bacterium from the periplasm into the extracellular medium. |
| GO:0015562 efflux transmembrane transporter activity | IDA PMID:19906986 Molecular basis of pyoverdine siderophore recycling in Pseud... | ACCEPT | Summary: PseudoCAP seed row for the PTN001253051 IBD (efflux transmembrane transporter activity). Seed verdict SOUND. Full text read: the evidence is mutant phenotype only, so IDA is the wrong code (see the parallel IMP row). Reason: The claim is right; the evidence code is not. Recorded as a PSEUDOCAP WRONG_EVIDENCE_CODE defect. Supporting Evidence: PMID:19906986 Therefore, the entire PvdRT-OpmQ system (i.e., the IM ABC transporter PvdT, the periplasmic fusion protein PvdR, and the OM porin OpmQ) appears to be involved in the transport of PVD from the periplasm to the extracellular milieu. |
| GO:0015562 efflux transmembrane transporter activity | IDA PMID:21035449 An efflux pump is involved in secretion of newly synthesized... | ACCEPT | Summary: PseudoCAP seed row for the PTN001253051 IBD (efflux transmembrane transporter activity). Seed verdict SOUND. The abstract shows the pump secretes newly made PVD; evidence is mutant microscopy and fractionation (IMP would be the stricter code; not filed because only the abstract was read). Reason: Supported export function of the pump. Supporting Evidence: PMID:21035449 Bacteria lacking this efflux pump accumulated PVD, or a fluorescent precursor, in the periplasm, due to their inability to efficiently secrete into the media newly synthesized PVD. |
| GO:0015562 efflux transmembrane transporter activity | IDA PMID:22187978 The PvdRT-OpmQ efflux pump controls the metal selectivity of... | ACCEPT | Summary: PseudoCAP seed row for the PTN001253051 IBD (efflux transmembrane transporter activity). Seed verdict SOUND. Abstract describes export of new and recycled PVD. Reason: Supported export function of the pump. Supporting Evidence: PMID:22187978 PvdRT-OpmQ is an ATP-dependent efflux pump involved in the secretion of newly synthesized pyoverdine (PVD) and of PVD that has transported and released its iron into the bacterium from the periplasm into the extracellular medium. |
| GO:0015562 efflux transmembrane transporter activity | IMP PMID:19906986 Molecular basis of pyoverdine siderophore recycling in Pseud... | ACCEPT | Summary: PseudoCAP seed row for the PTN001253051 IBD (efflux transmembrane transporter activity). Seed verdict SOUND. Mutants accumulate periplasmic PVD; complemented. Reason: Direct genetic evidence that the system exports PVD. Supporting Evidence: PMID:19906986 Conversely, PA2389 , PA2390 , and opmQ mutants accumulated five- to sixfold higher amounts of PVD than wild-type PAO1, suggesting an involvement of these genes in PVD export. PMID:19906986 Therefore, the entire PvdRT-OpmQ system (i.e., the IM ABC transporter PvdT, the periplasmic fusion protein PvdR, and the OM porin OpmQ) appears to be involved in the transport of PVD from the periplasm to the extracellular milieu. |
| GO:0015562 efflux transmembrane transporter activity | IMP PMID:22187978 The PvdRT-OpmQ efflux pump controls the metal selectivity of... | ACCEPT | Summary: PseudoCAP seed row for the PTN001253051 IBD (efflux transmembrane transporter activity). Seed verdict SOUND. Mutants accumulate PVD-metal complexes. Reason: Genetic evidence that the system exports PVD. Supporting Evidence: PMID:22187978 the PvdRT-OpmQ efflux pump exports unwanted metals complexed with PVD from the bacterium |
| GO:0015562 efflux transmembrane transporter activity | IMP PMID:23766114 An efflux pump is required for siderophore recycling by Pseu... | ACCEPT | Summary: PseudoCAP seed row for the PTN001253051 IBD (efflux transmembrane transporter activity). Seed verdict SOUND. Mutants fail to recycle PVD. Reason: Genetic evidence that the system exports PVD. Supporting Evidence: PMID:23766114 Mutation of genes encoding this efflux pump (named PvdRT-OpmQ) prevented recycling of PVDI from the periplasm into the extracellular medium. |
| GO:0016020 membrane | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro RND_pump_MFP mapping to membrane. Reason: True but entailed by GO:1990281 efflux pump complex (a membrane protein complex), accepted below. |
| GO:0019898 extrinsic component of membrane | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro MacA alpha-hairpin mapping. MFPs bridge the inner-membrane transporter and the outer-membrane channel from the periplasm. Reason: Plausible for a periplasmic MFP bound to the inner-membrane PvdT, but no membrane-association assay exists for PvdR; the complex term carries the useful information. Supporting Evidence: PMID:19906986 PvdRT-OpmQ displays the typical architecture of Gram-negative tripartite ABC-type exporters, consisting of an IM component with both ATPase and permease domains, a periplasmic membrane fusion protein, and a TolC-like OM protein |
| GO:0022857 transmembrane transporter activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro mapping to generic transporter activity. Reason: Entailed by GO:0015562 efflux transmembrane transporter activity, accepted above. |
| GO:0042597 periplasmic space | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular location (periplasm). PvdR has a predicted signal peptide and is the periplasmic fusion protein of the pump. Reason: Location where the MFP acts. Supporting Evidence: PMID:19906986 Therefore, the entire PvdRT-OpmQ system (i.e., the IM ABC transporter PvdT, the periplasmic fusion protein PvdR, and the OM porin OpmQ) appears to be involved in the transport of PVD from the periplasm to the extracellular milieu. |
| GO:0055085 transmembrane transport | IEA GO_REF:0000002 | MODIFY | Summary: InterPro mapping to generic transmembrane transport. Reason: True but general, and the substrate is known, so GO:0044718 siderophore transmembrane transport is the informative process: its definition is explicitly membrane-crossing and it is the only transmembrane-specific siderophore process term. Note that GO:0044718 is_a GO:0015891 only, and neither is a descendant of GO:0055085 (checked in go-basic.obo and QuickGO, 2026-11-06), so this refinement does not formally retain the transmembrane-transport ancestry; that looks like a missing is_a in GO and is raised as a question below. Proposed replacements: siderophore transmembrane transport Supporting Evidence: PMID:19906986 we identified a tripartite ATP-binding cassette efflux transporter, here named PvdRT-OpmQ, which translocates PVD from the periplasmic space to the extracellular milieu |
| GO:1990195 macrolide transmembrane transporter complex | IEA GO_REF:0000002 | REMOVE | Summary: InterPro MacA alpha-hairpin mapping to macrolide transmembrane transporter complex. PvdR is MacA-like in structure, but PvdRT-OpmQ gives no macrolide resistance. Reason: Wrong electronic transfer: the substrate is pyoverdine, and the full text reports no contribution to macrolide resistance. Supporting Evidence: PMID:19906986 the PvdRT-OpmQ efflux system does not provide any contribution to P. aeruginosa resistance to antibiotics belonging to the classes of tetracyclines, aminoglycosides, Ξ²-lactams and macrolides, and chloramphenicol |
| GO:1990281 efflux pump complex | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN001253051. Seeds are PvdR (self-seed, PseudoCAP) and Salmonella MdtA (Q8ZNQ3, IDA PMID:24960027). Stands on MdtA alone. Reason: PvdR is the MFP of the tripartite PvdRT-OpmQ pump. Supporting Evidence: PMID:19906986 Therefore, the entire PvdRT-OpmQ system (i.e., the IM ABC transporter PvdT, the periplasmic fusion protein PvdR, and the OM porin OpmQ) appears to be involved in the transport of PVD from the periplasm to the extracellular milieu. |
| GO:1990281 efflux pump complex | IDA PMID:19906986 Molecular basis of pyoverdine siderophore recycling in Pseud... | ACCEPT | Summary: PseudoCAP seed row for the PTN001253051 IBD (efflux pump complex). Seed verdict SOUND. Full text read: complex membership is inferred from the operon, architecture and identical mutant phenotypes, not from a direct assay; IDA is the wrong code. Reason: Membership in the tripartite pump is well founded; the IDA code is recorded as a PSEUDOCAP defect. Supporting Evidence: PMID:19906986 PvdRT-OpmQ displays the typical architecture of Gram-negative tripartite ABC-type exporters, consisting of an IM component with both ATPase and permease domains, a periplasmic membrane fusion protein, and a TolC-like OM protein |
| GO:1990281 efflux pump complex | IDA PMID:21035449 An efflux pump is involved in secretion of newly synthesized... | ACCEPT | Summary: PseudoCAP seed row for the PTN001253051 IBD (efflux pump complex). Seed verdict SOUND. Reason: Component of the PvdRT-OpmQ pump. Supporting Evidence: PMID:21035449 Bacteria lacking this efflux pump accumulated PVD, or a fluorescent precursor, in the periplasm, due to their inability to efficiently secrete into the media newly synthesized PVD. |
| GO:1990281 efflux pump complex | IDA PMID:22187978 The PvdRT-OpmQ efflux pump controls the metal selectivity of... | ACCEPT | Summary: PseudoCAP seed row for the PTN001253051 IBD (efflux pump complex). Seed verdict SOUND. Reason: Component of the PvdRT-OpmQ pump. Supporting Evidence: PMID:22187978 PvdRT-OpmQ is an ATP-dependent efflux pump involved in the secretion of newly synthesized pyoverdine (PVD) and of PVD that has transported and released its iron into the bacterium from the periplasm into the extracellular medium. |
| GO:1990281 efflux pump complex | IMP PMID:19906986 Molecular basis of pyoverdine siderophore recycling in Pseud... | ACCEPT | Summary: PseudoCAP seed row for the PTN001253051 IBD (efflux pump complex). Seed verdict SOUND. Each of the three mutants gives the same phenotype. Reason: Component of the PvdRT-OpmQ pump. Supporting Evidence: PMID:19906986 Therefore, the entire PvdRT-OpmQ system (i.e., the IM ABC transporter PvdT, the periplasmic fusion protein PvdR, and the OM porin OpmQ) appears to be involved in the transport of PVD from the periplasm to the extracellular milieu. |
| GO:1990281 efflux pump complex | IMP PMID:22187978 The PvdRT-OpmQ efflux pump controls the metal selectivity of... | ACCEPT | Summary: PseudoCAP seed row for the PTN001253051 IBD (efflux pump complex). Seed verdict SOUND. Reason: Component of the PvdRT-OpmQ pump. Supporting Evidence: PMID:22187978 the PvdRT-OpmQ efflux pump exports unwanted metals complexed with PVD from the bacterium |
| GO:1990281 efflux pump complex | IMP PMID:23766114 An efflux pump is required for siderophore recycling by Pseu... | ACCEPT | Summary: PseudoCAP seed row for the PTN001253051 IBD (efflux pump complex). Seed verdict SOUND. Reason: Component of the PvdRT-OpmQ pump. Supporting Evidence: PMID:23766114 Mutation of genes encoding this efflux pump (named PvdRT-OpmQ) prevented recycling of PVDI from the periplasm into the extracellular medium. |
| GO:1990961 xenobiotic detoxification by transmembrane export across the plasma membrane | IEA GO_REF:0000002 | REMOVE | Summary: InterPro MacA alpha-hairpin mapping to xenobiotic detoxification by export. PvdRT-OpmQ exports the cell's own siderophore. Reason: Contradicted: the pump gives no resistance to five antibiotic classes; its substrate is endogenous pyoverdine and PVD-metal complexes, not xenobiotics. Supporting Evidence: PMID:19906986 the PvdRT-OpmQ efflux system does not provide any contribution to P. aeruginosa resistance to antibiotics belonging to the classes of tetracyclines, aminoglycosides, Ξ²-lactams and macrolides, and chloramphenicol |
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Download this section (compressed HTML)Q: GO:0044718 siderophore transmembrane transport is_a GO:0015891 siderophore transport only, and neither term is a descendant of GO:0055085 transmembrane transport, although the definition of GO:0044718 is explicitly membrane-crossing and sibling terms such as GO:0034219 carbohydrate transmembrane transport do sit under GO:0055085. Should GO:0044718 gain that is_a, so that refining a GO:0055085 row to it keeps the transmembrane claim?
Q: Has the PvdRT-OpmQ complex been shown physically (co-purification, cross-linking or structure), or does membership rest on the operon and shared mutant phenotypes?
Q: Should MFPs of tripartite pumps carry contributes_to rather than enables for efflux transmembrane transporter activity, given that the MFP alone does not move substrate across a membrane?
Experiment: Reconstitute PvdT with PvdR in proteoliposomes and measure ATPase stimulation and pyoverdine-dependent activity; pull down PvdR with PvdT and OpmQ from iron-starved PAO1 membranes.
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