PA1257 is the integral inner-membrane permease subunit of a polar-amino-acid ABC transporter of Pseudomonas aeruginosa PAO1, with four predicted transmembrane helices and the binding-protein-dependent transport (ABC_TM1) domain. It is encoded in an operon with the ATP-binding subunit PA1256 and the periplasmic substrate-binding protein PA1260. Transposon mutants in each of these three genes grow poorly on hydroxy-L-proline as sole carbon source but not on L-proline, and the operon is induced by hydroxy-L-proline, so the system is a hydroxyproline importer that feeds the bacterium's hydroxyproline catabolic pathway. Whether it also takes up other amino acids, such as the cystine carried by its closest E. coli relative TcyL, has not been tested.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | ACCEPT | Summary: Plasma-membrane IBD at PTN000770157, seeded by E. coli permease subunits. Reason: Four predicted TM helices and an ABC_TM1 permease domain; the bacterial inner membrane is the plasma membrane. Supporting Evidence: file:PSEAE/PA1257/PA1257-uniprot.txt FT TRANSMEM 20..42 FT /note="Helical" |
| GO:0005886 plasma membrane | IEA GO_REF:0000120 | ACCEPT | Summary: Combined electronic mapping (cell inner membrane). Reason: Same claim as the IBA row, supported by the predicted TM helices. Supporting Evidence: file:PSEAE/PA1257/PA1257-uniprot.txt FT TRANSMEM 20..42 FT /note="Helical" |
| GO:0015184 L-cystine transmembrane transporter activity | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: IBA from PTN000770175, whose only seed is E. coli TcyL. PA1257 is not a seed. The only experimental data on PA1257 point to hydroxy-L-proline, not cystine. The topology (checked with panther_tree.py on 2026-11-05) shows an 18-leaf Proteobacteria SPECIATION node mixing permeases of several specificities, with PA1257 in a Pseudomonas-specific duplication (PTN002413080) and the cystine-specific seeds confined to the Enterobacteriaceae clade PTN002024099. Reason: Substrate choice in binding-protein-dependent amino acid ABC systems is set largely by the periplasmic binding protein, and the PA1256-PA1257-PA1260 system is induced by, and needed for growth on, hydroxy-L-proline. The cystine specificity of TcyL is therefore not known to be inherited by this permease. Cystine transport by PA1257 has not been tested, so this is over-annotation rather than a refuted claim. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN000770175 · PTN000770175 SUPPORTS SOURCE BUT NOT TARGET The node carries an L-cystine IBD seeded only by E. coli TcyL, but it is an 18-leaf Proteobacteria SPECIATION clade of mixed specificity (two HORIZ_TRANSFER subtrees and three lineage-specific duplications). The target belongs to a hydroxyproline-induced operon with its own binding protein, so the specific substrate is not shared across the node. UniProtKB:P0AFT2 · E. coli TcyL (EcoCyc IDA/IGI) SUPPORTS SOURCE BUT NOT TARGET Sound for TcyL itself. Supporting Evidence: PMID:18833300 Knockouts in these genes affected growth on hydroxy-L-proline as a carbon source, and expression of all three genes was induced by hydroxy-L-proline (Table 2 and 3). PMID:18833300 three genes are part of a single operon (PA1256, PA1257 and PA1260) which was predicted to be involved in amino acid transport and instead found to be involved in Hydroxy-L-Proline transport |
| GO:0015811 L-cystine transport | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: Process counterpart of the GO:0015184 IBA, from the same TcyL-only node. Reason: Same argument as the GO:0015184 row; the GO_CENTRAL CHECK defect recorded there covers this row. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN000770175 · PTN000770175 SUPPORTS SOURCE BUT NOT TARGET As for the GO:0015184 row. Supporting Evidence: PMID:18833300 There was no growth defect on L-proline, nor was expression affected by L-proline as an inducer, suggesting specificity for hydroxy-L-proline. |
| GO:0016020 membrane | IEA GO_REF:0000120 | TOO GENERAL | Summary: InterPro-based membrane mapping. Reason: True, but GO:0005886 plasma membrane, accepted in this review, is_a membrane. |
| GO:0022857 transmembrane transporter activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping from the amino acid ABC permease signature. Reason: Correct but general. PA1257 is the permease of an ATP-binding-cassette amino acid importer (TIGR01726, with ATPase PA1256 and binding protein PA1260); hydroxyproline is an amino acid in GO (GO:0034590 is_a GO:0015179). GO:0015424 is the supported specific term. Proposed replacements: ABC-type amino acid transporter activity Supporting Evidence: PMID:18833300 PA1256, PA1257 and PA1260 are all components of a predicted ABC amino acid transporter encoded in a putative operon along with two hypothetical genes. file:PSEAE/PA1257/PA1257-uniprot.txt TIGR01726; HEQRo_perm_3TM |
| GO:0034589 hydroxyproline transport | IMP PMID:18833300 High-throughput phenotypic characterization of Pseudomonas a... | ACCEPT | Summary: PseudoCAP row and the PA1257 seeding of PTN000770157 (GO:0006865). A PAO1 transposon mutant of this permease is defective for growth on hydroxy-L-proline, and the operon is induced by hydroxy-L-proline but not L-proline. Reason: Seed verdict SOUND (full text read). There is no direct uptake assay, but a permease-subunit mutant with a substrate-specific growth defect, matched by substrate-specific induction of the whole operon, is genetic evidence of the transport the protein performs. The node IBD also stands on E. coli TcyL and GlnP. Supporting Evidence: PMID:18833300 Knockouts in these genes affected growth on hydroxy-L-proline as a carbon source, and expression of all three genes was induced by hydroxy-L-proline (Table 2 and 3). PMID:18833300 There was no growth defect on L-proline, nor was expression affected by L-proline as an inducer, suggesting specificity for hydroxy-L-proline. |
| GO:0043190 ATP-binding cassette (ABC) transporter complex | IEA GO_REF:0000120 | MODIFY | Summary: Combined electronic mapping to the ABC transporter complex. Reason: Correct but general. The operon encodes a periplasmic substrate-binding protein (PA1260), so the complex is the binding-protein-dependent type, GO:0055052 (is_a GO:0043190). Proposed replacements: ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing Supporting Evidence: PMID:18833300 PA1256, PA1257 and PA1260 are all components of a predicted ABC amino acid transporter encoded in a putative operon along with two hypothetical genes. |
| GO:0055085 transmembrane transport | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping. Reason: Correct but general. GO:0034589 hydroxyproline transport is not a descendant of transmembrane transport, so the specific supported term on this branch is GO:0003333 amino acid transmembrane transport (is_a GO:0055085). Proposed replacements: amino acid transmembrane transport Supporting Evidence: PMID:18833300 three genes are part of a single operon (PA1256, PA1257 and PA1260) which was predicted to be involved in amino acid transport and instead found to be involved in Hydroxy-L-Proline transport |
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Download this section (compressed HTML)Experiment: Measure uptake of radiolabelled trans-4-hydroxy-L-proline, L-proline and L-cystine in PAO1, the PA1257 mutant and the complemented mutant, and test binding of these substrates by purified PA1260.
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The substrate range of the PA1256-PA1257-PA1260 transporter is unknown beyond the hydroxy-L-proline growth phenotype: direct uptake, stereoisomer preference (trans-4- versus cis-4- or 3-hydroxyproline) and any cystine transport, as by its E. coli relative TcyL, have not been measured.
BIOLOGY
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