PA0920 (Q9I537) notes

Review session 2026-10-28 (PseudoCAP IBA-seed protocol, worklist rank 37)

No deep-research provider was available; these notes are my own reading of the UniProt record, the cited
paper and four further Braunschweig (Moser lab) papers found by PubMed search and cached with
just fetch-pmid. Only PMID:21392131 has full text in the cache; the others are abstract-only (the PubMed
MCP returned no PMC full text for PMC4553816 beyond the abstract and Significance statement).

Identity

P. aeruginosa PAO1 locus PA0920, UniProt Q9I537 (unreviewed), 881 aa; 14 predicted TM helices
(residues 36-542) followed by the cytoplasmic LPG_synthase_C catalytic domain (Pfam PF09924, residues
565-853); Pfam PF03706 LPG_synthase_TM; NCBIfam NF033480 bifunc_MprF; PANTHER PTHR34697:SF2.
The UniProt name "Phosphatidylglycerol lysyltransferase" (EC 2.3.2.3) and the lysyl-tRNA catalytic
activity line are ARBA predictions (ECO:0000256|ARBA). They are wrong for this protein: PA0920 is the
alanyl-phosphatidylglycerol synthase (A-PGS).

Literature

Discovery: P. aeruginosa makes alanyl-PG under acidic growth PMID:19087229. Deletion abolishes it
PMID:19087229 and
heterologous expression confers it on E. coli PMID:19087229. In vitro activity PMID:19087229; inner
membrane location PMID:19087229; acid-induced transcription PMID:19087229.
Mechanism: the C-terminal domain is the minimal catalytic core PMID:21392131; the
PG head group is specifically recognised PMID:21392131. Immunogold places the epitope at the cytosolic face of the inner
membrane PMID:21392131.
Structure (the PseudoCAP-cited paper): crystal structure of the A-PGS catalytic domain, tunnel for PG and
aminoacyl-tRNA, substrate recognition with misacylated tRNAs PMID:26261323; PMID:26261323. "Lipid homeostasis" appears only in the general framing
PMID:26261323; the paper does not measure lipid levels or their maintenance in cells.
Specificity: P. aeruginosa naturally makes A-PG, not L-PG PMID:22267511. A-PGS and L-PGS specificity is not encoded in an obvious motif PMID:22267511, a caution for
propagating the alanyl-specific term by phylogeny.
Homeostasis is set by a second enzyme: the periplasmic A-PG hydrolase PA0919, encoded downstream, tunes
A-PG levels PMID:23792962; PMID:23792962.

Is 'phospholipid homeostasis' PA0920's own process?

No. GO:0055091 is the maintenance of a steady-state phospholipid level. PA0920 performs one biosynthetic
step: it transfers alanine from Ala-tRNA(Ala) to PG, making A-PG. The steady state (acid-dependent level of
A-PG) emerges from the synthase together with acid-regulated transcription and the PA0919 hydrolase; the
"lipid homeostasis" wording in the cited paper's abstract is framing, not a reported result (full text not read). The gene's own process is A-PG
synthesis, i.e. GO:0008654 phospholipid biosynthetic process (no aminoacyl-PG-specific GO term exists; an
NTR could be requested). The homeostasis term is therefore a consequence-level over-annotation for PA0920.

It is worse at the node: QuickGO (2026-10-28) shows PTN002162750 passes GO:0055091 to 26 leaves, among
them the fungal ergosteryl-3beta-O-glycine synthases ErgS of Aspergillus fumigatus (Q4WB70) and
Yarrowia lipolytica (Q6C7J3), whose UniProt function (PubMed:35131263) is tRNA-dependent glycylation of
ergosterol, a sterol, not a phospholipid. The leaves also include S. aureus, B. subtilis and Listeria
MprF (L-PGS), M. tuberculosis LysX2 (Rv1619), Streptomyces and green-algal proteins. None of the
comparator leaves carries an experimental GO annotation; all their function annotations come from PA0920.

Annotation decisions

GO:0047637 phosphatidylglycerol alanyltransferase activity (IDA PseudoCAP; IBA): ACCEPT, core MF.
GO:0050071 phosphatidylglycerol lysyltransferase activity (IEA from ARBA EC 2.3.2.3): REMOVE; the enzyme
is the alanyl-specific synthase and P. aeruginosa makes no L-PG. Defect recorded against UniProt/ARBA.
GO:0055091 phospholipid homeostasis (IDA PseudoCAP; IBA): MODIFY to GO:0008654 phospholipid
biosynthetic process. PseudoCAP and GO_CENTRAL defects recorded.
GO:0005886 plasma membrane (IEA SubCell): ACCEPT; direct evidence (PMID:19087229, PMID:21392131).

PseudoCAP IBA-seed assessment

Leaf counts in QuickGO (2026-10-28) differ from the worklist (older PAINT release): PTN002162750 now carries
26 GO:0055091 and 24 GO:0016755 leaves; PTN005059806 carries 55 GO:0047637 leaves (diverse bacteria,
Myxococcus, Planctomycetes, the archaeon Methanosarcina acetivorans Q8TMG3), each also getting the two
upper-node terms.

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN002162750	GO:0055091 phospholipid homeostasis	1 (sole)	14 (12 taxa) in worklist; 26 in QuickGO	GO:0055091, IDA, PMID:26261323 (PseudoCAP)	WRONG	The abstract describes a crystal structure and in vitro substrate-recognition study and no homeostasis data (full text not read). PA0920's own process is A-PG biosynthesis; homeostasis is a system-level consequence involving the PA0919 hydrolase. The node also contains ergosteryl-glycine synthases (ErgS) that do not modify phospholipids, so the term is wrong for part of the clade even if read loosely.
PTN002162750	GO:0016755 aminoacyltransferase activity	1 (sole)	12 (10 taxa) in worklist; 24 in QuickGO	GO:0047637, IDA, PMID:26261323 (PseudoCAP)	SOUND	Direct in vitro tRNA-dependent alanylation of PG by the A-PGS catalytic domain (also PMID:19087229, PMID:21392131). The generic aminoacyl-transfer term fits every known member (A-PGS, L-PGS, ErgS all transfer an aminoacyl group from aminoacyl-tRNA to a lipid).
PTN005059806	GO:0047637 phosphatidylglycerol alanyltransferase activity	1 (sole)	2 (2 taxa) in worklist; 55 in QuickGO	GO:0047637, IDA, PMID:26261323 (PseudoCAP)	SOUND	Seed is direct biochemistry, and A-PGS sequences form a recognisable group (PMID:22267511). Caveat: Arendt et al. report that A-PG vs L-PG specificity is not marked by a sequence motif, so with one seed and now 55 leaves the alanyl-specific node term should be re-checked against the nine orthologs whose specificity that paper determined.

Audit 2026-10-29: confidence matched to what was read

PMID:26261323 is still abstract-only: the PubMed MCP returns abstract and
Significance only for PMC4553816, and PMC/Europe PMC/PNAS full text was not
retrievable. The PSEUDOCAP WRONG_TERM defect (homeostasis IDA -> phospholipid
biosynthetic process) rests on the abstract describing no homeostasis assay,
so it is lowered from PROBABLE to SUSPECTED. The GO_CENTRAL defect on
PTN002162750 stays PROBABLE: besides the seed paper, it rests on positive
facts (QuickGO leaves include sterol-modifying ErgS enzymes). The UNIPROT EC
defect stays CONFIRMED: the PMID:19087229 abstract states the decisive fact
outright (DeltaPA0920 loses A-PG; the protein was named A-PG synthase).
PMID:26261323 reference correctness changed from MISCITED to UNVERIFIED.
No action changes.