plcH / PA0844 (P06200) review notes

Summary of the literature

PlcH (PHLC_PSEAE, reviewed) is a 730-residue precursor with a 38-residue signal peptide and a
mature chain 39-730. UniProt: [file:PSEAE/plcH/plcH-uniprot.txt "Hydrolyzes sphingomyelin in
addition to phosphatidylcholine."] and "Predicted to be exported by the Tat system". PANTHER places
it in PTHR31956 (non-specific phospholipase C-related), with the plant NPC enzymes and the
M. tuberculosis PlcA-D proteins — the superfamily the 2002 paper names.

Primary data:

Stonehouse et al. 2002 PMID:12410824, abstract read. PMID:12410824; the enzyme purifies as a 1:1 PlcH-PlcR2 heterodimer;
PMID:12410824; and on haemolysis, PMID:12410824 — i.e. haemolysis by the purified enzyme was measured.
Ostroff, Vasil & Vasil 1990 PMID:2120196, abstract read: PMID:2120196, while PLC-N also acts on
phosphatidylserine. This is the paper behind the PseudoCAP GO:0016298 lipase row.
Luberto et al. 2003 PMID:12799377, abstract read: SM synthase activity is secreted
PMID:12799377, and PMID:12799377, lost in
plcH operon knockouts.
Voulhoux et al. 2001 PMID:11726509, abstract read: PMID:11726509. PlcH is cargo of the Xcp T2SS.
Jackson et al. 2013 PMID:23667230, full text cached and read: PMID:23667230 and PMID:23667230.
PC catabolites choline and glycine betaine activate the Anr regulon. No haemolysis assay
appears anywhere in the cached text, which matters for the GO:0044179 IMP row keyed to it.

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?
PTN001277539	GO:0004629 C-type glycerophospholipase activity	9	253 (49 taxa)	GO:0034480, IDA, PMID:12410824 (PseudoCAP)	SOUND	Purified, 1,500-fold enriched enzyme, assayed on defined substrates, active only on choline phospholipids. A PC-PLC is by definition a C-type glycerophospholipase, so the node term is a correct generalisation of the seed.	M. tuberculosis PlcA/B/C/D (P9WIB5, P9WIB3, P9WIB1, P9WIA9 — IDA GO:0004629 and EXP/IMP GO:0034480) and four Arabidopsis NPC genes (AT2G26870, AT3G48610, AT3G03540, AT3G03530) — UniProt accessions verified by live QuickGO query 2026-11-05	Yes. Four mycobacterial seeds carry their own IDA/EXP evidence for the same chemistry. No GO_CENTRAL defect; the node term fits a clade whose plant members are non-specific PLCs.
PTN001277563	GO:0034480 phosphatidylcholine phospholipase C activity	5	11 (5 taxa)	GO:0034480, IDA, PMID:12410824 (PseudoCAP)	SOUND	Same seed, same direct assay; here the node term is exactly the seed term and the node is small (11 leaf IBAs, 5 taxa) — the bacterial PC-PLC subfamily.	The same four M. tuberculosis Plc enzymes, each with EXP GO:0034480 (PMID:20736081) and IMP GO:0034480 (PMID:12100560)	Yes. The IBD would stand on the mycobacterial seeds alone. No GO_CENTRAL defect.

Both PseudoCAP seed rows are the same GOA row (enables GO:0034480 IDA PMID:12410824), and it
is sound. The defects filed on this gene concern two other PseudoCAP rows (below).

Consistency with the reviewed PLD genes in this repository: genes/PSEAE/pldA and
genes/PSEAE/PA5089 are D-type phospholipases on a different PANTHER family and share no node
with plcH, so nothing is duplicated there.

Annotation decisions and defects

GO:0034480 (IDA, IBA, IEA): ACCEPT. Core function.
GO:0004629, GO:0016298 (IDA), GO:0016788: TOO_GENERAL — all entailed by GO:0034480.
GO:0033188 sphingomyelin synthase activity (IDA): KEEP_AS_NON_CORE. Real activity of the
purified protein, genetically tied to plcH, but a secreted enzyme does not meet the
cytoplasmic-leaflet substrate pools of a true SM synthase, and the physiological output is
hydrolysis. Treated as a genuine secondary activity of the same catalytic machinery
(projects/ENZYME_SPECIFICITY.md tiering), not as noise.
GO:0015628 protein secretion by the type II secretion system (IDA): MARK_AS_OVER_ANNOTATED
plus a PSEUDOCAP WRONG_TERM defect (PROBABLE). PlcH is Xcp cargo; the term belongs to the
machinery. Identical calls already exist on genes/PSEAE/lasB and genes/PSEAE/lap, and the
defect text cross-references them.
GO:0016042 lipid catabolic process (IEA): MODIFY to GO:0034638 phosphatidylcholine catabolic
process.
GO:0044179 hemolysis in another organism: ACCEPT on both rows (consistency), since the claim
is directly supported by the purified-enzyme haemolysis data. On the IMP row keyed to
PMID:23667230 a PSEUDOCAP WRONG_REFERENCE defect is filed at PROBABLE: the cached full text
of that paper reports colonization, biofilm, Anr and mouse-pneumonia phenotypes and no
haemolysis experiment. Confidence is PROBABLE rather than CONFIRMED because figure panels are
not captured in the cached extraction.
NEW GO:0005576 extracellular region (IC): the gene had no cellular component annotation at
all, and two independent lines agree (activity purified from culture supernatants; Tat signal
peptide plus Xcp-dependent secretion).