PA5377 (CbcW) is the integral inner-membrane permease subunit of the Cbc (choline/betaine/carnitine) ABC importer, encoded in the cbcXWV operon (PA5378-PA5376) with the substrate-binding protein CbcX and the ATPase CbcV. It has six transmembrane helices and belongs to the ChoW/ProW family of binding protein-dependent permeases. The CbcWV core transporter works with several separately encoded periplasmic binding proteins that set its substrate specificity. With CbcX it takes up choline (and betaine), with BetX glycine betaine, and with CaiX L-carnitine and short-chain acylcarnitines. Cbc imports these quaternary ammonium compounds mainly for use as carbon and nitrogen sources. Transposon mutants in PA5377 cannot grow on choline, glycine betaine or carnitine as sole carbon sources. Expression of cbcXWV is induced by glycine betaine through the activator GbdR.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005275 amine transmembrane transporter activity | IBA GO_REF:0000033 | MODIFY | Summary: PAINT IBA from PTN000766131, seeded by PA5377 (PseudoCAP IDA, PMID:19919675) and E. coli ProW (P14176). Reason: The transport is real, but the term is on the wrong branch. GO defines amine transmembrane transporter activity for weakly basic amino or substituted-amino compounds. Choline, glycine betaine and carnitine (and ProW's glycine betaine and proline betaine) are quaternary ammonium compounds, which GO places under GO:0015651 and GO:0015418, not under amine transporter activity. The right MF for the clade is ABC-type quaternary ammonium compound transporting activity. For a permease subunit this is a complex-level activity, recorded as contributes_to in core_functions. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000766131 · PTN000766131 SUPPORTS TRANSFER PTHR47737 node (Bacteria; 13 leaf IBAs in 11 taxa) of ProW/ChoW-type QAC permeases. A QAC ABC transporter term suits it, but the amine term does not. UniProtKB:Q9HTI7 · PA5377 SUPPORTS TRANSFER The target's own PseudoCAP IDA is a seed, which is expected, not circular. The evidence supports QAC transport, not amine transport. UniProtKB:P14176 · ProW (E. coli) SUPPORTS TRANSFER ProU transports glycine betaine and proline betaine, which are also QACs. Proposed replacements: ABC-type quaternary ammonium compound transporting activity Supporting Evidence: PMID:19919675 The PA5376::tn, PA5377::tn and PA5378::tn mutants all failed to grow on choline (Fig. 3A) and betaine (Fig. S2) as sole C sources PMID:19919675 Interestingly, cells of MKH13 transformed with pME6041 expressing cbcXWV from PAO1, pCbcPAO1, accumulated choline and betaine but little to no carnitine. |
| GO:0005275 amine transmembrane transporter activity | IDA PMID:19919675 The ATP-binding cassette transporter Cbc (choline/betaine/ca... | MODIFY | Summary: PseudoCAP IDA, a co-seed of the PTN000766131 amine transporter IBD. Reason: The paper shows Cbc-dependent uptake of choline, betaine and carnitine (quaternary ammonium compounds), with PA5377 required. The right GO branch is quaternary ammonium compound transport, not amine transport. Proposed replacements: ABC-type quaternary ammonium compound transporting activity Supporting Evidence: PMID:19919675 the deficiencies in choline uptake by PA14 mutants with insertions in individual cbc loci were complemented by cbcXWV from either PAO1 or B728a |
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | ACCEPT | Summary: SubCell mapping from cell membrane, multi-pass. Reason: PA5377 is a six-helix integral inner-membrane permease of a binding protein-dependent ABC importer. Supporting Evidence: file:PSEAE/PA5377/PA5377-uniprot.txt Multi-pass membrane protein |
| GO:0015226 carnitine transmembrane transporter activity | IBA GO_REF:0000033 | MODIFY | Summary: PAINT IBA from PTN000766131, whose sole seed is PA5377 (PseudoCAP IDA, PMID:19919675). Reason: Carnitine uptake through Cbc in P. aeruginosa is real, but it depends on the separately encoded carnitine-specific SBP CaiX (PA5388), not on the permease. Strains with a 98-100% identical Cbc core but no CaiX (P. syringae DC3000) do not transport carnitine, and E. coli ProW in the same node is not a carnitine transporter. A carnitine-specific MF is therefore over-specific both for the permease and for the clade. The activity of CbcW is best captured as contributing to ABC-type quaternary ammonium compound transport, with specificity set by the partner SBP. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: ROLE CONFLATION GRANULARITY MISMATCH Sources checked: PANTHER:PTN000766131 · PTN000766131 SUPPORTS SOURCE BUT NOT TARGET The carnitine specificity of the seed depends on the trans-encoded CaiX SBP, which most clade members need not have. UniProtKB:Q9HTI7 · PA5377 SUPPORTS TRANSFER The target's own IDA is the sole seed, which is expected, not circular. It is true for PA5377 only in combination with CaiX. Proposed replacements: ABC-type quaternary ammonium compound transporting activity Supporting Evidence: PMID:19919675 A plasmid expressing only the core transporter, pNcbcWV, was constructed by deleting cbcX from pNcb-cXWV; it restored carnitine uptake to BT (Fig. 5), consistent with an association between the native CaiX SBP and the core transporter. PMID:19919675 yet B728a transports carnitine and DC3000 does not |
| GO:0015226 carnitine transmembrane transporter activity | IDA PMID:19919675 The ATP-binding cassette transporter Cbc (choline/betaine/ca... | MODIFY | Summary: PseudoCAP IDA, the sole seed of the PTN000766131 carnitine transporter IBD. Reason: The paper shows that PAO1 CbcWV supports carnitine uptake only with the CaiX SBP. CbcXWV alone in E. coli takes up choline and betaine but not carnitine. For the permease, the accurate MF is the broader QAC ABC transport activity it contributes to; carnitine is one SBP-defined substrate, and the process term carnitine transmembrane transport is kept. Proposed replacements: ABC-type quaternary ammonium compound transporting activity Supporting Evidence: PMID:19919675 These findings provide compelling evidence that Psyr_2916 and PA5388, hereafter referred to as CaiX, enable Cbc-mediated carnitine uptake in P. syringae and P. aeruginosa respectively. |
| GO:0015837 amine transport | IEA GO_REF:0000108 | MODIFY | Summary: Inter-ontology inference from the amine transmembrane transporter activity rows. Reason: This row inherits the wrong-branch amine term. The substrates are quaternary ammonium compounds, and the corresponding process is quaternary ammonium group transport (glycine betaine and carnitine transport are its descendants). Proposed replacements: quaternary ammonium group transport Supporting Evidence: PMID:19919675 These transposon mutants also failed to grow on L-carnitine (Fig. S2), suggesting that carnitine is an additional substrate for this transporter. |
| GO:0015838 amino-acid betaine transport | IDA PMID:19919675 The ATP-binding cassette transporter Cbc (choline/betaine/ca... | MODIFY | Summary: PseudoCAP IDA to the parent of glycine betaine and carnitine transport. Reason: Correct but general. Both specific descendants are supported in the same paper and already carried by the gene, glycine betaine transport and carnitine transmembrane transport. Proposed replacements: glycine betaine transport carnitine transmembrane transport Supporting Evidence: PMID:19919675 These transposon mutants also failed to grow on L-carnitine (Fig. S2), suggesting that carnitine is an additional substrate for this transporter. |
| GO:0015871 choline transport | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA from PTN000766131, whose sole seed is PA5377 (PseudoCAP IMP, PMID:19919675). Reason: Choline is the main CbcXWV substrate (CbcX binds choline with high affinity). The PA5377 mutant cannot grow on choline and its choline uptake defect is complemented by PAO1 cbcXWV. TIGR03416 defines the ChoXWV choline permease family. Leaves in the ProW part of the node may transport choline only weakly, but the IBA on PA5377 is well supported. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000766131 · PTN000766131 SUPPORTS TRANSFER ChoW/ProW clade. Choline transport is reasonable for the ChoXWV members. UniProtKB:Q9HTI7 · PA5377 SUPPORTS TRANSFER The target's own IMP is the sole seed, which is expected, not circular. Supporting Evidence: PMID:19919675 the deficiencies in choline uptake by PA14 mutants with insertions in individual cbc loci were complemented by cbcXWV from either PAO1 or B728a file:PSEAE/PA5377/PA5377-uniprot.txt ABC_choXWV_perm |
| GO:0015871 choline transport | IMP PMID:19919675 The ATP-binding cassette transporter Cbc (choline/betaine/ca... | ACCEPT | Summary: PseudoCAP IMP from the PA14 PA5377::tn mutant. Reason: Direct mutant evidence. PA5377::tn fails to grow on choline as sole carbon source, and choline uptake by the cbc mutants is restored by PAO1 cbcXWV. Supporting Evidence: PMID:19919675 The PA5376::tn, PA5377::tn and PA5378::tn mutants all failed to grow on choline (Fig. 3A) and betaine (Fig. S2) as sole C sources PMID:19919675 the deficiencies in choline uptake by PA14 mutants with insertions in individual cbc loci were complemented by cbcXWV from either PAO1 or B728a |
| GO:0016020 membrane | IEA GO_REF:0000120 | MODIFY | Summary: Combined IEA membrane. Reason: True but general. The gene already carries plasma membrane, the specific location of this inner-membrane permease. Proposed replacements: plasma membrane Supporting Evidence: file:PSEAE/PA5377/PA5377-uniprot.txt Multi-pass membrane protein |
| GO:0031457 glycine betaine catabolic process | IDA PMID:19919675 The ATP-binding cassette transporter Cbc (choline/betaine/ca... | MARK AS OVER ANNOTATED | Summary: PseudoCAP IDA to glycine betaine catabolism, based on the inability of the cbc mutants to grow on betaine as a carbon source. Reason: PA5377 is a permease. It imports betaine but performs no step of betaine demethylation, which is done by GbcAB and downstream enzymes. Loss of growth on betaine is an indirect phenotype of loss of uptake. The transport itself is captured by glycine betaine transport. Supporting Evidence: PMID:19919675 The PA5376::tn, PA5377::tn and PA5378::tn mutants all failed to grow on choline (Fig. 3A) and betaine (Fig. S2) as sole C sources |
| GO:0031460 glycine betaine transport | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA from PTN000766131, seeded by PA5377 and E. coli ProW. Reason: Glycine betaine transport is a well-supported property of both seeds, ProU in E. coli and Cbc (with CbcX or BetX) in P. aeruginosa, and suits the ProW/ChoW clade. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000766131 · PTN000766131 SUPPORTS TRANSFER Two independent experimental seeds from different genera. UniProtKB:Q9HTI7 · PA5377 SUPPORTS TRANSFER The target's own IDA is a seed, which is expected, not circular. Supporting Evidence: PMID:19919675 Interestingly, cells of MKH13 transformed with pME6041 expressing cbcXWV from PAO1, pCbcPAO1, accumulated choline and betaine but little to no carnitine. |
| GO:0031460 glycine betaine transport | IDA PMID:19919675 The ATP-binding cassette transporter Cbc (choline/betaine/ca... | ACCEPT | Summary: PseudoCAP IDA from heterologous uptake assays with PAO1 cbcXWV. Reason: PAO1 CbcXWV confers betaine uptake on transporter-deficient E. coli MKH13, and the PA5377 mutant cannot grow on betaine. Supporting Evidence: PMID:19919675 Interestingly, cells of MKH13 transformed with pME6041 expressing cbcXWV from PAO1, pCbcPAO1, accumulated choline and betaine but little to no carnitine. |
| GO:0031460 glycine betaine transport | IDA PMID:21478341 Roles of three transporters, CbcXWV, BetT1, and BetT3, in Ps... | ACCEPT | Summary: PseudoCAP IDA citing Malek et al. 2011 (abstract only in cache). Reason: The claim is well supported for PA5377 by PMID:19919675. The abstract of PMID:21478341 concerns choline uptake and GbdR/betaine induction of cbcXWV, and the betaine-uptake data the curator used cannot be seen, so this is deferred to the curator. Supporting Evidence: PMID:21478341 cbcXWV expression was induced by the activator GbdR and glycine betaine PMID:19919675 Interestingly, cells of MKH13 transformed with pME6041 expressing cbcXWV from PAO1, pCbcPAO1, accumulated choline and betaine but little to no carnitine. |
| GO:0031460 glycine betaine transport | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA prediction of glycine betaine transport. Reason: The rule is unvetted, but the claim is supported experimentally (PMID:19919675). Supporting Evidence: PMID:19919675 Interestingly, cells of MKH13 transformed with pME6041 expressing cbcXWV from PAO1, pCbcPAO1, accumulated choline and betaine but little to no carnitine. |
| GO:0042426 choline catabolic process | IDA PMID:19919675 The ATP-binding cassette transporter Cbc (choline/betaine/ca... | MARK AS OVER ANNOTATED | Summary: PseudoCAP IDA to choline catabolism, from the growth defect of cbc mutants on choline. Reason: The permease imports choline for catabolism but does not oxidise it. BetA and BetB do that. The growth defect on choline is an indirect consequence of lost uptake, already captured by choline transport. Supporting Evidence: PMID:19919675 The PA5376::tn, PA5377::tn and PA5378::tn mutants all failed to grow on choline (Fig. 3A) and betaine (Fig. S2) as sole C sources |
| GO:0042426 choline catabolic process | IDA PMID:21478341 Roles of three transporters, CbcXWV, BetT1, and BetT3, in Ps... | MARK AS OVER ANNOTATED | Summary: PseudoCAP IDA to choline catabolism citing Malek et al. 2011. Reason: The abstract itself frames the paper as about choline uptake transporters supporting growth on choline, which is an indirect phenotype for a catabolic-process term. The transporter does not catabolise choline. Supporting Evidence: PMID:21478341 BetT3 and CbcXWV, but not BetT1, were sufficient to support growth on choline. |
| GO:0043190 ATP-binding cassette (ABC) transporter complex | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA from PTN000766131, seeded by PA5377 and E. coli ProW. Reason: The TMD of a binding protein-dependent ABC importer is by definition part of the ABC transporter complex, and this is safe for the whole clade. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000766131 · PTN000766131 SUPPORTS TRANSFER All members are ABC permease TMDs. UniProtKB:Q9HTI7 · PA5377 SUPPORTS TRANSFER The target's own IDA is a seed, which is expected, not circular. Supporting Evidence: file:PSEAE/PA5377/PA5377-uniprot.txt ABC_transptr_choline_permease |
| GO:0043190 ATP-binding cassette (ABC) transporter complex | IDA PMID:19919675 The ATP-binding cassette transporter Cbc (choline/betaine/ca... | ACCEPT | Summary: PseudoCAP IDA to the ABC transporter complex. Reason: CbcWV acts as a core transporter with interchangeable SBPs (CbcX, BetX, CaiX). The complex was inferred from function rather than isolated, but the claim is sound. Supporting Evidence: PMID:19919675 A plasmid expressing only the core transporter, pNcbcWV, was constructed by deleting cbcX from pNcb-cXWV; it restored carnitine uptake to BT (Fig. 5), consistent with an association between the native CaiX SBP and the core transporter. |
| GO:0043190 ATP-binding cassette (ABC) transporter complex | IEA GO_REF:0000104 | ACCEPT | Summary: UniRule transfer of ABC transporter complex. Reason: Consistent with family membership and the experimental rows. Supporting Evidence: file:PSEAE/PA5377/PA5377-uniprot.txt ABC_transptr_choline_permease |
| GO:0055085 transmembrane transport | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro2GO from the MetI-like permease domain. Reason: True but uninformative. Carnitine transmembrane transport (GO:1902603), accepted in this review, entails it, and the specific QAC transport processes are recorded elsewhere. Supporting Evidence: file:PSEAE/PA5377/PA5377-uniprot.txt Multi-pass membrane protein |
| GO:1901682 sulfur compound transmembrane transporter activity | IDA PMID:23763788 The widespread plant-colonizing bacterial species Pseudomona... | UNDECIDED | Summary: PseudoCAP IDA citing a P. syringae bioreporter paper (abstract only in cache). Reason: The abstract describes P. syringae QAC bioreporters and plant-derived choline. It mentions neither sulfur compounds nor PA5377, and no full text is available. The sulfur compound may be choline-O-sulfate or a sulfonium analogue transported by Cbc, but this cannot be verified, so the row is left to the curator. Supporting Evidence: PMID:23763788 Whole-cell bacterial bioreporters of the phytopathogen Pseudomonas syringae were constructed that couple a QAC-responsive transcriptional fusion with well-characterized bacterial QAC transporters. |
| GO:1902495 transmembrane transporter complex | IDA PMID:19919675 The ATP-binding cassette transporter Cbc (choline/betaine/ca... | MODIFY | Summary: PseudoCAP IDA to the generic transporter complex. Reason: Correct but general. The specific descendant, ATP-binding cassette (ABC) transporter complex, is supported by the same paper and already carried. Proposed replacements: ATP-binding cassette (ABC) transporter complex Supporting Evidence: PMID:19919675 A plasmid expressing only the core transporter, pNcbcWV, was constructed by deleting cbcX from pNcb-cXWV; it restored carnitine uptake to BT (Fig. 5), consistent with an association between the native CaiX SBP and the core transporter. |
| GO:1902603 carnitine transmembrane transport | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA from PTN000766131, whose sole seed is PA5377 (PseudoCAP IDA, PMID:21478341). Reason: For PA5377 the claim is true. The PA5377 mutant cannot grow on carnitine, PAO1 CbcWV restores carnitine uptake in a CaiX-containing host, and CaiX-CbcWV imports carnitine and short-chain acylcarnitines. The node-level propagation is over-specific, however. Carnitine transport depends on the trans-encoded SBP CaiX, which most clade members need not have, and the near-identical DC3000 Cbc does not transport carnitine. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: ROLE CONFLATION Sources checked: PANTHER:PTN000766131 · PTN000766131 SUPPORTS SOURCE BUT NOT TARGET True for the seed, but SBP-dependent and so not a clade-wide property of the permease. UniProtKB:Q9HTI7 · PA5377 SUPPORTS TRANSFER The target's own IDA is the sole seed, which is expected, not circular. Supporting Evidence: PMID:19919675 These transposon mutants also failed to grow on L-carnitine (Fig. S2), suggesting that carnitine is an additional substrate for this transporter. PMID:29517479 Short-chain acylcarnitines are imported by the ABC transporter CaiX-CbcWV. |
| GO:1902603 carnitine transmembrane transport | IDA PMID:21478341 Roles of three transporters, CbcXWV, BetT1, and BetT3, in Ps... | ACCEPT | Summary: PseudoCAP IDA citing Malek et al. 2011, the sole seed of the carnitine-transport IBD. Reason: The claim is true for PA5377 (PMID:19919675, PMID:29517479). The cited paper's abstract concerns only choline uptake, and its full text could not be retrieved, so whether it contains carnitine uptake data for CbcXWV is unknown. The row is accepted, and the reference flagged for checking. Supporting Evidence: PMID:19919675 A plasmid expressing only the core transporter, pNcbcWV, was constructed by deleting cbcX from pNcb-cXWV; it restored carnitine uptake to BT (Fig. 5), consistent with an association between the native CaiX SBP and the core transporter. |
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Download this section (compressed HTML)Q: Should the PTN000766131 IBDs be revised? The amine transporter term is on the wrong branch for quaternary ammonium substrates, and carnitine specificity depends on the trans-encoded CaiX SBP rather than on the permease clade.
Q: Does PMID:21478341 contain carnitine or glycine betaine uptake data for CbcXWV, or should the PseudoCAP carnitine row be re-keyed to PMID:19919675?
Q: What sulfur compound underlies the PseudoCAP GO:1901682 IDA from PMID:23763788 (for example choline-O-sulfate), and was PAO1 cbcXWV used in that study?
Experiment: Test whether CbcWV transports choline-O-sulfate or dimethylsulfoniopropionate by radiolabelled uptake in a QAC transporter-deficient host expressing PAO1 cbcWV with each of the SBPs (CbcX, BetX, CaiX), to resolve the sulfur compound transporter claim and to map SBP-dependent specificity.
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