SpuE (PA0301) is a periplasmic spermidine-binding protein of the PotD/PotF family in Pseudomonas aeruginosa, a substrate-binding component, with its paralog SpuD, of the SpuDEFGH ABC transporter for polyamine uptake. SpuE binds spermidine with nanomolar affinity and does not bind putrescine, cadaverine or spermine; Trp271 is a key determinant of this specificity. Mutation of spuE greatly reduces spermidine uptake and lowers induction of the type III secretion system by polyamines.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0015846 polyamine transport | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO from the spermidine/putrescine-binding signature. Reason: Correct but general; consistent with the IMP row. SpuE binds only spermidine and the spuE mutant is defective in spermidine uptake, so the specific descendant GO:0015848 spermidine transport is supported. Proposed replacements: spermidine transport |
| GO:0015846 polyamine transport | IMP PMID:12081945 Functional analysis and regulation of the divergent spuABCDE... | MODIFY | Summary: PseudoCAP seed row. The full text shows spermidine uptake greatly reduced in the spuE mutant. Seed verdict SOUND; the term is correct for the gene and for the PTN001249912 clade. Reason: Sound but general. Uptake data and exclusive spermidine binding support GO:0015848 spermidine transport (is_a GO:0015846). Proposed replacements: spermidine transport Supporting Evidence: PMID:12081945 Second, spermidine uptake is inducible in spermidine-grown cells and is greatly reduced in either spuD or spuE mutant (Fig. |
| GO:0015847 putrescine transport | IBA GO_REF:0000033 | REMOVE | Summary: IBA from PTN008624361, seeded by E. coli PotF and PotD. SpuE does not bind putrescine, so it does not take part in putrescine uptake. Reason: Over-propagation to a specificity-diverged paralog. The binding protein of an ABC importer determines its substrate, and SpuE binds spermidine only. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN008624361 · PTN008624361 SUPPORTS SOURCE BUT NOT TARGET PotD/PotF clade node; putrescine transport is right for PotF, PotD and SpuD but not for the spermidine-only SpuE branch. UniProtKB:P31133 · E. coli PotF SUPPORTS SOURCE BUT NOT TARGET Putrescine-specific binding protein; specificity differs from SpuE. UniProtKB:P0AFK9 · E. coli PotD SUPPORTS SOURCE BUT NOT TARGET Binds spermidine and putrescine; SpuE has lost putrescine binding. Supporting Evidence: file:PSEAE/spuE/spuE-uniprot.txt Binds spermidine with high affinity (KD=14.3 nM). Does not bind putrescine, cadaverine or spermine. |
| GO:0019808 polyamine binding | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro2GO polyamine binding. Reason: Entailed by GO:0019809 spermidine binding (is_a GO:0019808), accepted below. |
| GO:0019809 spermidine binding | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN008624361, seeded by E. coli PotD (IDA) and the IDA on Q9I6J0 itself (expected, not circular). The IBD stands without this seed. Reason: Core activity, shown by ITC and a spermidine-bound crystal structure. Supporting Evidence: PMID:22300763 we found that SpuD is a putrescine-preferential binding protein, while SpuE binds to spermidine exclusively. |
| GO:0019809 spermidine binding | IDA PMID:22300763 Structural basis of substrate binding specificity revealed b... | ACCEPT | Summary: PseudoCAP seed row. The abstract states SpuE binds spermidine exclusively and reports a SpuE-spermidine structure. Reason: Seed verdict SOUND. Supporting Evidence: file:PSEAE/spuE/spuE-uniprot.txt Binds spermidine with high affinity (KD=14.3 nM). |
| GO:0019810 putrescine binding | IBA GO_REF:0000033 | REMOVE | Summary: IBA from PTN008624361, seeded by SpuD, PotF and PotD. Contradicted for SpuE, which binds spermidine exclusively. Reason: Directly contradicted by binding measurements on SpuE itself; a Trp271Phe change is needed to give SpuE putrescine affinity. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN008624361 · PTN008624361 SUPPORTS SOURCE BUT NOT TARGET Node term is right for the seeds (SpuD, PotF, PotD) but SpuE has lost putrescine binding; no NOT is placed on its branch. UniProtKB:Q9I6J1 · SpuD (IDA PMID:22300763) SUPPORTS SOURCE BUT NOT TARGET Same paper shows SpuD binds putrescine and SpuE does not. UniProtKB:P31133 · E. coli PotF SUPPORTS SOURCE BUT NOT TARGET Putrescine-binding protein with experimental support. UniProtKB:P0AFK9 · E. coli PotD SUPPORTS SOURCE BUT NOT TARGET Binds putrescine and spermidine. Supporting Evidence: PMID:22300763 we found that SpuD is a putrescine-preferential binding protein, while SpuE binds to spermidine exclusively. PMID:22300763 substitution of Trp271 by Phe enabled SpuE to gain substantial binding affinity for putrescine |
| GO:0030288 outer membrane-bounded periplasmic space | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN008624361; SpuE has a 24-residue signal peptide. Reason: Correct location for a Gram-negative periplasmic solute-binding protein. |
| GO:0042597 periplasmic space | IEA GO_REF:0000120 | TOO GENERAL | Summary: Combined IEA periplasm. Reason: Entailed by GO:0030288 outer membrane-bounded periplasmic space (is_a GO:0042597), accepted above. |
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Download this section (compressed HTML)Q: Is the reduced type III secretion induction of the spuE mutant due to lower spermidine import, or does SpuE signal to the T3SS regulators directly?
Experiment: Test whether the SpuE Trp271Phe variant, which gains putrescine binding, confers putrescine uptake through SpuFGH in a spuD background.
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