PA3891 is the ATP-binding (nucleotide-binding domain) subunit of an OpuC-type osmoprotectant ABC importer encoded by PA3888-PA3891, together with two distinct permeases (PA3888, PA3890) and a periplasmic glycine betaine-binding protein (PA3889). It is a soluble protein that sits on the cytoplasmic face of the inner membrane and has an N-terminal ABC ATPase domain followed by tandem CBS domains, the feature that marks osmoregulatory quaternary-amine ABC transporters. A PAO1 genomic clone carrying PA3891 restored osmoprotected growth under high salt to a P. syringae mutant lacking its own OpuC ATPase. By analogy with the characterised P. syringae OpuC, the transporter imports glycine betaine with high affinity and choline with low affinity, and may accept other quaternary ammonium compounds such as carnitine and proline betaine, which accumulate as compatible solutes under osmotic stress.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000166 nucleotide binding | IEA GO_REF:0000104 | MODIFY | Summary: UniRule transfer of generic nucleotide binding to an ABC transporter ATPase. Reason: True but less specific than the evidence supports. The NBD has a Walker A motif annotated as an ATP-binding site, and the gene already carries ATP binding (GO:0005524), which is the specific nucleotide. Proposed replacements: ATP binding Supporting Evidence: file:PSEAE/PA3891/PA3891-uniprot.txt ABC_transporter-like_ATP-bd |
| GO:0000166 nucleotide binding | ISS PMID:17660277 Characterization of the osmoprotectant transporter OpuC from... | MODIFY | Summary: PseudoCAP ISS from P. syringae DC3000 OpuCA (Q87WH5, PSPTO_4575). Reason: Same claim as the IEA row. The bound nucleotide of an ABC ATPase is ATP, which the gene already carries (GO:0005524). Proposed replacements: ATP binding Supporting Evidence: PMID:17660277 Tandem cystathionine-Ξ²-synthase (CBS) domains in the ATP-binding component of OpuC were required for transporter function. |
| GO:0005524 ATP binding | IEA GO_REF:0000120 | ACCEPT | Summary: Combined IEA from the ABC transporter NBD signatures. Reason: PA3891 has a complete ABC NBD with a Walker A ATP-binding site (residues 39-46) and the ABC signature motif. ATP binding is intrinsic to the subunit and needed for its transport-driving activity. Supporting Evidence: file:PSEAE/PA3891/PA3891-uniprot.txt ABC_transporter-like_ATP-bd |
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA from PTN001953445, whose sole seed is PA3891 itself, through a PseudoCAP IDA to the ABC transporter complex (PMID:17660277). Reason: The location is right for this protein. An ABC importer NBD acts at the cytoplasmic face of the inner membrane, as UniRule also states, and is_active_in is the right qualifier for a peripheral subunit. The seed is weak, however. PMID:17660277 shows only that a PAO1 genomic clone carrying PA3891 restores osmoprotected growth to a P. syringae mutant. It does not assay localisation or complex formation. The IBA is kept because the claim is biologically sound for the whole OpuC-type NBD clade, but it rests on no experimental localisation. Propagation Review Root cause: SOURCE WEAK OR INFERRED Failure modes: SOURCE EVIDENCE WEAK Sources checked: PANTHER:PTN001953445 Β· PTN001953445 SUPPORTS TRANSFER PTHR43117 clade with 31 leaf IBAs in 24 taxa. The node term suits a clade of ABC importer NBDs. UniProtKB:Q9HXC2 Β· PA3891 SOURCE WEAK OR INFERRED The target is the sole seed, which is expected, not circular. Its experimental evidence is heterologous growth complementation, not localisation. Supporting Evidence: file:PSEAE/PA3891/PA3891-uniprot.txt Cell inner membrane PMID:17660277 The sequence of the complementing clones indicated that transporters involving Psyr4249 from P. syringae pv. syringae strain B728a and PA3891 from P. aeruginosa PAO1 were functional, as predicted. |
| GO:0005886 plasma membrane | IEA GO_REF:0000120 | ACCEPT | Summary: UniRule/SubCell mapping to plasma membrane, from cell inner membrane (peripheral). Reason: Consistent with the IBA row. The NBD is a peripheral subunit of an inner-membrane ABC importer. Supporting Evidence: file:PSEAE/PA3891/PA3891-uniprot.txt Cell inner membrane |
| GO:0006970 response to osmotic stress | IEA GO_REF:0000117 | MODIFY | Summary: ARBA prediction of response to osmotic stress. Reason: The claim is sound. The CBS-domain OpuC-type transporters import osmoprotectants under high salt, and PA3891 complemented osmoprotected growth on 0.5 M NaCl. However, the gene already carries the more specific GO:0071475 cellular hyperosmotic salinity response (PseudoCAP, PMID:17660277), which is the condition actually tested. Proposed replacements: cellular hyperosmotic salinity response Supporting Evidence: PMID:17660277 the transformants were plated on MinA media containing 0.5 M NaCl and either glycine betaine or choline (2 mM) |
| GO:0015226 carnitine transmembrane transporter activity | ISS PMID:17660277 Characterization of the osmoprotectant transporter OpuC from... | KEEP AS NON CORE | Summary: PseudoCAP ISS from DC3000 OpuCA. In that paper carnitine is a substrate of the DC3000 OpuC transporter. Reason: For DC3000 OpuC, carnitine was inferred from inhibition of [14C]betaine and [14C]choline uptake and from weak osmoprotection, not from direct carnitine uptake. Nothing was tested for the PAO1 transporter. Carnitine is plausibly a minor substrate of a broad-specificity OpuC system. Glycine betaine is the main substrate, and GO:0015418 covers the broad specificity. Supporting Evidence: PMID:17660277 Taken together, these results confirm that OpuC mediates the uptake of multiple substrates, including glycine betaine, choline, proline betaine, carnitine, and acetylcholine. |
| GO:0015418 ABC-type quaternary ammonium compound transporting activity | IDA PMID:17660277 Characterization of the osmoprotectant transporter OpuC from... | ACCEPT | Summary: PseudoCAP IDA from PMID:17660277. The only PA3891 experiment is heterologous complementation of osmoprotected growth. Reason: The term fits the broad quaternary-amine specificity of OpuC-type transporters (betaine, choline, carnitine, proline betaine, acetylcholine for the DC3000 ortholog). PA3891 complemented a DC3000 strain lacking the OpuC ATPase, which shows that it can drive osmoprotectant uptake. As an NBD, PA3891 contributes this activity together with its permease and binding-protein partners. The evidence is functional complementation rather than a direct assay. This is noted but not filed separately here; see the seeding rows. Supporting Evidence: PMID:17660277 The sequence of the complementing clones indicated that transporters involving Psyr4249 from P. syringae pv. syringae strain B728a and PA3891 from P. aeruginosa PAO1 were functional, as predicted. file:PSEAE/PA3891/PA3891-uniprot.txt Reaction=a quaternary ammonium(out) + ATP + H2O = a quaternary ammonium(in) + ADP + phosphate + H(+) |
| GO:0015418 ABC-type quaternary ammonium compound transporting activity | IEA GO_REF:0000003 | ACCEPT | Summary: EC2GO mapping from EC 7.6.2.9 (quaternary amine ABC transporter), assigned by UniRule. Reason: Consistent with the IDA row and with the CBS-domain OpuC-type NBD family (TIGR01186, IPR005892). Supporting Evidence: file:PSEAE/PA3891/PA3891-uniprot.txt Gly-betaine_transp_ATP-bd |
| GO:0015838 amino-acid betaine transport | IDA PMID:17660277 Characterization of the osmoprotectant transporter OpuC from... | MODIFY | Summary: PseudoCAP IDA to the parent of glycine betaine transport. Reason: Correct but general. The specific supported descendant is glycine betaine transport (GO:0031460), which the gene already carries. Carnitine transport, the other descendant, rests only on competition data for the ortholog and is kept as non-core. Proposed replacements: glycine betaine transport Supporting Evidence: PMID:17660277 one, designated OpuC, functioned as the primary or sole transporter for glycine betaine and as one of multiple transporters for choline under high osmolarity |
| GO:0015871 choline transport | IEA GO_REF:0000108 | KEEP AS NON CORE | Summary: Inter-ontology inference from the ISS row ABC-type choline transporter activity. Reason: The DC3000 ortholog OpuC is a low-affinity choline transporter and one of several choline transporters in that strain. In P. aeruginosa, choline uptake is dominated by BetT1, BetT3 and CbcXWV (PMID:21478341). Choline uptake by the PA3888-PA3891 system is plausible but minor. Supporting Evidence: PMID:17660277 The P. syringae pv. tomato OpuC transporter had a high affinity for glycine betaine, a low affinity for choline, and a broad substrate specificity that included acetylcholine, carnitine, and proline betaine. |
| GO:0016020 membrane | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO membrane. Reason: True but general. The specific location is the cytoplasmic face of the inner (plasma) membrane, which the gene already carries. Proposed replacements: plasma membrane Supporting Evidence: file:PSEAE/PA3891/PA3891-uniprot.txt Cell inner membrane |
| GO:0016887 ATP hydrolysis activity | IEA GO_REF:0000120 | ACCEPT | Summary: Combined IEA from the ABC NBD signatures. Reason: ATP hydrolysis is the subunit-intrinsic activity of the NBD that powers substrate translocation by the complex. The CBS domains of this ATPase were shown to be required for function in the ortholog. Supporting Evidence: file:PSEAE/PA3891/PA3891-uniprot.txt ABC_transporter-like_ATP-bd |
| GO:0031459 ABC-type glycine betaine transporter activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA from PTN001953060, whose sole seed is PA3891 itself (PseudoCAP IDA, PMID:17660277). Reason: Glycine betaine is the main, high-affinity substrate of the characterised P. syringae ortholog (Q87WH5 OpuCA, uptake and competition assays). PA3891 complemented osmoprotected growth of an opuCA-deficient P. syringae strain, so the claim is plausible for PA3891 and for an OpuC-type CBS-NBD clade. For an NBD subunit the activity is that of the complex. GO's convention of enables on ABC subunits is accepted here, and core_functions records it as contributes_to. The seed itself is indirect, because no betaine transport assay was done with PA3891 and the selection plates contained either betaine or choline. Propagation Review Root cause: SOURCE WEAK OR INFERRED Failure modes: SOURCE EVIDENCE WEAK Sources checked: PANTHER:PTN001953060 Β· PTN001953060 SUPPORTS TRANSFER PTHR43117 clade with 23 leaf IBAs in 18 taxa. A glycine betaine ABC transporter term is reasonable for OpuC-type CBS-domain NBDs. UniProtKB:Q9HXC2 Β· PA3891 SOURCE WEAK OR INFERRED The target is the sole seed, which is expected, not circular. Its evidence is heterologous growth complementation, and the substrate specificity is transferred from the P. syringae ortholog. Supporting Evidence: PMID:17660277 one, designated OpuC, functioned as the primary or sole transporter for glycine betaine and as one of multiple transporters for choline under high osmolarity PMID:17660277 The sequence of the complementing clones indicated that transporters involving Psyr4249 from P. syringae pv. syringae strain B728a and PA3891 from P. aeruginosa PAO1 were functional, as predicted. |
| GO:0031459 ABC-type glycine betaine transporter activity | IDA PMID:17660277 Characterization of the osmoprotectant transporter OpuC from... | ACCEPT | Summary: PseudoCAP IDA, the sole seed of the PAINT IBD at PTN001953060. Reason: The claim is plausible, as for the IBA row, but the evidence code is overstated. The only PA3891 experiment is functional complementation of osmoprotected growth in P. syringae. No glycine betaine uptake was measured for PA3891, and the selection used betaine or choline. Glycine betaine specificity comes from the DC3000 ortholog characterised in the same paper. IGI (complementation) or ISS (with Q87WH5) would describe the evidence correctly. Supporting Evidence: PMID:17660277 the transformants were plated on MinA media containing 0.5 M NaCl and either glycine betaine or choline (2 mM) PMID:17660277 The sequence of the complementing clones indicated that transporters involving Psyr4249 from P. syringae pv. syringae strain B728a and PA3891 from P. aeruginosa PAO1 were functional, as predicted. |
| GO:0031460 glycine betaine transport | IDA PMID:17660277 Characterization of the osmoprotectant transporter OpuC from... | ACCEPT | Summary: PseudoCAP IDA to glycine betaine transport. Reason: This is the core process of the PA3888-PA3891 OpuC-type importer by orthology and complementation. As for the MF row, the evidence for PA3891 itself is complementation rather than a direct uptake assay. Supporting Evidence: PMID:17660277 one, designated OpuC, functioned as the primary or sole transporter for glycine betaine and as one of multiple transporters for choline under high osmolarity |
| GO:0031460 glycine betaine transport | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO from IPR005892 (glycine betaine transporter ATP-binding subunit). Reason: Consistent with family membership and with the PseudoCAP row. Supporting Evidence: file:PSEAE/PA3891/PA3891-uniprot.txt Gly-betaine_transp_ATP-bd |
| GO:0033266 ABC-type choline transporter activity | ISS PMID:17660277 Characterization of the osmoprotectant transporter OpuC from... | KEEP AS NON CORE | Summary: PseudoCAP ISS from DC3000 OpuCA. Reason: The DC3000 OpuC transports choline with low affinity, and the PAO1 complementation screen used either choline or betaine. Choline is a plausible but secondary substrate. In P. aeruginosa, choline uptake relies mainly on BetT1, BetT3 and CbcXWV. Supporting Evidence: PMID:17660277 The P. syringae pv. tomato OpuC transporter had a high affinity for glycine betaine, a low affinity for choline, and a broad substrate specificity that included acetylcholine, carnitine, and proline betaine. |
| GO:0043190 ATP-binding cassette (ABC) transporter complex | IDA PMID:17660277 Characterization of the osmoprotectant transporter OpuC from... | ACCEPT | Summary: PseudoCAP IDA to the ABC transporter complex. This row is the seed (through PAINT) of the plasma membrane IBD at PTN001953445. Reason: Membership of an ABC importer complex is correct for an NBD encoded with two permeases and an SBP (PA3888-PA3890). UniRule states the expected 2 NBD + 2 TMD + SBP composition. The paper did not isolate or otherwise demonstrate the complex, so IDA overstates the evidence. Supporting Evidence: file:PSEAE/PA3891/PA3891-uniprot.txt The complex is probably composed of two ATP-binding proteins, two transmembrane proteins and a solute-binding protein. PMID:17660277 The sequence of the complementing clones indicated that transporters involving Psyr4249 from P. syringae pv. syringae strain B728a and PA3891 from P. aeruginosa PAO1 were functional, as predicted. |
| GO:0071475 cellular hyperosmotic salinity response | IDA PMID:17660277 Characterization of the osmoprotectant transporter OpuC from... | KEEP AS NON CORE | Summary: PseudoCAP IDA from the high-salt complementation screen. Reason: Osmoprotectant import is the means by which this transporter contributes to growth at high salinity, and the PA3891 clone restored growth on 0.5 M NaCl plus betaine or choline. The process is the physiological context of the transport activity rather than the gene's core function, which is quaternary-amine transport. The evidence is heterologous genetic complementation. Supporting Evidence: PMID:17660277 the transformants were plated on MinA media containing 0.5 M NaCl and either glycine betaine or choline (2 mM) |
| GO:1902603 carnitine transmembrane transport | IEA GO_REF:0000108 | KEEP AS NON CORE | Summary: Inter-ontology inference from the ISS row carnitine transmembrane transporter activity. Reason: This row follows the ISS MF. Carnitine is a possible minor substrate, inferred from competition assays on the DC3000 ortholog. In P. aeruginosa, carnitine uptake is carried out mainly by CaiX-CbcWV (PMID:19919675). Supporting Evidence: PMID:17660277 Taken together, these results confirm that OpuC mediates the uptake of multiple substrates, including glycine betaine, choline, proline betaine, carnitine, and acetylcholine. |
Loading supporting contentβ¦
Download this section (compressed HTML)Q: Should the PseudoCAP IDA rows for PA3891 citing PMID:17660277 be re-coded as IGI (heterologous functional complementation) or ISS with Q87WH5? They are the sole seeds of two PAINT IBDs (PTN001953060, PTN001953445).
Q: Which substrates does the PAO1 PA3888-PA3891 transporter actually take up (glycine betaine, choline, proline betaine, carnitine), and which osmoprotectant did the complementing PAO1 clone rescue on?
Experiment: Measure [14C]glycine betaine, choline and carnitine uptake in PAO1 PA3891 deletion mutants (alone and combined with cbcXWV and betT1/betT3 deletions) under hyperosmotic conditions, with competition assays to define the substrate range of the PA3888-PA3891 transporter.
Loading supporting contentβ¦
Download this section (compressed HTML)Loading supporting contentβ¦
Download this section (compressed HTML)