pscC (PA1716, Q9I319) review notes

Review session 2026-10-28 (PseudoCAP IBA-seed protocol)

Fetched with just fetch-gene PSEAE pscC; accession Q9I319 matches the worklist entry (rank 43,
PA1716). The entry is UniProtKB/TrEMBL (unreviewed), annotated by HAMAP-Rule MF_02219, with
protein existence "Inferred from homology". No deep-research provider key was available, so these
notes are manual, from the cached publications, the UniProt record and the cached PAINT table
interpro/panther/PTHR30332/PTHR30332-paint.tsv.

What PscC is

PscC (SctC) is the outer-membrane secretin of the P. aeruginosa type III secretion system
(T3SS, injectisome): the ring-forming channel of the base through which effectors leave the
bacterium. UniProt (HAMAP-Rule MF_02219): "Forms a ring-shaped multimeric structure with an
apparent central pore in the outer membrane"; "Belongs to the bacterial secretin family. T3SS
SctC subfamily"; NCBIfam TIGR02516 (type_III_yscC), PANTHER PTHR30332:SF5.
The membrane-inserted multimer has been purified and imaged: cryo-EM of cell-free-synthesised
PscC gives a barrel with a "cup and saucer" architecture and a plugged central chamber, closely
similar to the T2SS secretin PulD [PMID:25156426 "The membrane-inserted, multimeric regions of
PscC, the" Pseudomonas aeruginosa type III secretion system secretin ... "of two distinct rings,
with that of PulD being less segmented than that of PscC."].
Its outer-membrane localisation has been examined directly in PAO1 depletion strains
PMID:22147293, where
PscC levels fall on LolB depletion but are little affected by BamA depletion.
The gene was identified in the exsD-pscB-L operon of the T3SS locus, whose members are
homologues of the Yersinia Ysc export apparatus, and transposon insertions in that region
abolish exoenzyme S production [PMID:8971719 "isolated which exhibited an exoenzyme S-deficient
phenotype (388::Tn5Tc 469," "unique. The other 11 ORFs demonstrated high homology to the YscB-L
proteins of" the yersiniae].
Later work used pscC mutants as the standard secretion-apparatus-defective control and
described the gene accordingly: "mutant in pscC, encoding a structural component of the type III
translocase" PMID:12421316; "or pscC, which encodes" an essential component of the secretion
apparatus, significantly attenuated in a mouse pneumonia model PMID:14977975; plasmid
insertion in pscC reduces T3SS-mediated killing of endothelial cells PMID:12385743.

PseudoCAP row details

GO:0030254 IMP PMID:8971719 (Yahr, Goranson & Frank 1996) is the sole seed of the
PTN009110345 IBD for this term (25 leaf IBAs over 15 taxa). The cached record is abstract-only
and does not say which of the twelve ORFs the mapped Tn5Tc insertions (469, 550) lie in, so the
gene-level attribution cannot be confirmed from what is available here; the curator read the
full text. The claim itself is not in doubt: the operon is the T3SS export apparatus, and three
independent later studies treat pscC mutants as secretion-apparatus-null (PMID:12421316,
PMID:14977975, PMID:12385743). No source defect is recorded - this is exactly the case where the
repository guidance says not to second-guess an experimental annotation whose full text we have
not read.
Note the contrast with the xcp cluster: the xcpQ/xcpR/xcpX GO:0015628 rows are keyed to a
review article (PMID:9818381) and so carry a wrong evidence code, whereas this row is keyed to a
primary transposon-mutagenesis paper and the evidence code is appropriate.

PAINT node context

interpro/panther/PTHR30332/PTHR30332-paint.tsv shows PTN009110345 carrying both T3SS terms -
GO:0030254 sole-seeded by this gene (Q9I319) and GO:0030257 seeded by another T3SS secretin
(P35672) - while the T2SS terms sit on a separate node, PTN000768388 (seeded by XcpQ and two other
P. aeruginosa secretins). An IRD at the child node PTN009110348 withdraws both T3SS terms in a
subclade (taxon:3880), so the curators have actively pruned the propagation rather than letting
the family root carry secretion-system-specific terms. That is the right shape for a family that
mixes T2SS secretins, T3SS secretins and other NolW-like channels.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN009110345	GO:0030254 protein secretion by the type III secretion system	1 (sole seed)	25 (15 taxa)	GO:0030254, IMP, PMID:8971719	SOUND	The term is right for an SctC secretin, and PscC specifically is treated as the T3SS secretion-apparatus component whose loss abolishes effector secretion and attenuates virulence (PMID:12421316, PMID:14977975, PMID:12385743); the purified multimer is the T3SS outer-membrane channel (PMID:25156426). The node is the T3SS-specific subnode of PTHR30332, with an IRD pruning a divergent subclade, so the term suits the clade that inherits it. Caveat, not a defect: the cached abstract of the seed paper does not pin the transposon insertions to pscC, so the gene-level attribution rests on the curator's reading of the full text.
PTN001251149	GO:0009306 protein secretion	2 (not sole)	0	GO:0030254, IMP, PMID:8971719	SOUND (term)	The generic parent term is true of PscC, and the node carries no leaf IBAs, so nothing propagates from it.

Open questions

No experimental annotation exists for the outer-membrane location of PscC in PAO1 even though
PMID:22147293 assays it directly in depletion strains; the location rows are all HAMAP/UniRule
or InterPro mappings. A curation-level gap rather than a knowledge gap.
Whether the plug and hairpin seen in the cell-free-synthesised PscC multimer (PMID:25156426)
reflect the gated state of the assembled injectisome base is unresolved.