spuA (PA0297, Q9I6J4) review notes

Review session 2026-11-05 (PseudoCAP IBA-seed protocol, tier 2)

Fetched with just fetch-gene PSEAE Q9I6J4 --alias spuA; accession matches the worklist.
Unreviewed entry. No deep-research provider was used. Literature: the cached seed paper
(abstract in cache; I read the PMC full text, PMC3147493, online), the cached full text of
Lu et al. 2002 (PMID:12081945, also the spuD/spuE source), and the 2021 SpuA structure paper
(PMID:34605433, cached with ai-gene-review fetch-pmid, abstract only). PubMed search was down
(NCBI 500); the structure paper was found through Europe PMC search.

Literature

PMID:12081945 (Lu et al. 2002, full text cached): the spuA mutant phenotype originates here
PMID:12081945.
PMID:21622750 (Yao et al. 2011, the PseudoCAP-cited paper). The abstract does not mention spuA.
In the full text (read online, not in the cache) spuA is renamed pauD1, the only E. coli PuuD
homologue in PAO1 (44% identity), and the spuA phenotype is restated as earlier work ("we
reported previously that a lesion in pauD1 (spuA) causes a significant growth defect on Spd
but not Put"). The 2011 paper constructed pauA mutants, not a new spuA mutant, so the IMP
experiment is in PMID:12081945. Recorded as a PSEUDOCAP WRONG_REFERENCE defect, PROBABLE.
PMID:34605433 (Chen et al. 2021): PMID:34605433; crystal structures
with a glutamyl thioester intermediate place it in the class I glutamine amidotransferase
family. A comparator class I GATase from M. smegmatis uses glutamine instead.
Consistency with spuD/spuE (genes/PSEAE/spuD, spuE): those are the periplasmic binding
proteins of the spuDEFGH transporter in the same locus; they sit in a different PANTHER family
and do not share PTN000230196. Both reviews accept spermidine/putrescine uptake; this review's
catabolic reading of spuA is consistent with them (uptake by SpuDEFGH, gamma-glutamylation
catabolism by SpuI/SpuB/SpuA).

Other seed of PTN000230196

E. coli PuuD P76038, queried live in QuickGO 2026-11-05: GO:0009447 putrescine catabolic process
(IMP, PMID:16499623) and GO:0033969 gamma-glutamyl-gamma-aminobutyrate hydrolase activity (IDA,
PMID:15590624). PuuD alone supports the polyamine catabolic process node term.

Annotation decisions

GO:0033969 (IBA, IEA): ACCEPT, core MF (activity assays, PMID:34605433).
GO:0016787, GO:0016811 (IEA): TOO_GENERAL (GO:0033969 is_a GO:0016811).
GO:0046203 spermidine catabolic process (IMP, seed): ACCEPT; citation defect only.
GO:0006598 polyamine catabolic process (IBA): TOO_GENERAL (entailed by GO:0046203).
GO:0006541 L-glutamine metabolic process (IEA, UniRule): MARK_AS_OVER_ANNOTATED; SpuA prefers
gamma-Glu-GABA, and glutamine use is the comparator enzyme's property.
Not added: GO:0009447 putrescine catabolic process. SpuA catalyses the last step of the
putrescine gamma-glutamylation route, but the spuA mutant grows normally on putrescine, so I
leave this as a question.
Action counts: ACCEPT 3, TOO_GENERAL 3, MARK_AS_OVER_ANNOTATED 1.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale	other seeds	IBD stands without this seed?
PTN000230196	GO:0006598 polyamine catabolic process	2	17 (13 taxa)	GO:0046203 spermidine catabolic process, IMP, PMID:21622750 (PseudoCAP)	SOUND	spuA mutant is defective in spermidine utilization, and SpuA hydrolyses gamma-Glu-GABA, a step of the gamma-glutamylation polyamine pathway, so it does part of the work. The cited paper restates the result; the experiment is in PMID:12081945 (WRONG_REFERENCE, PROBABLE).	E. coli PuuD P76038 (IMP putrescine catabolic process; IDA GO:0033969)	Yes; node term suits a PuuD-like clade

PSEUDOCAP defects: 1 (WRONG_REFERENCE, PROBABLE). No GO_CENTRAL defect.