pqsH (PA2587, Q9I0Q0) review notes

No deep-research API was available, so these notes come from manual literature
research (cached publications plus a PubMed search on "PqsH Pseudomonas aeruginosa
monooxygenase", 2026-10-28).

Biology

PqsH is the terminal enzyme of PQS biosynthesis. It hydroxylates HHQ at C3 to
give PQS, using NADH and O2 PMID:20662781.
Purified MBP-PqsH was characterised biochemically. Kinetics confirm HHQ, NADH
and O2 as substrates. NADPH also works, with about 20-fold lower kcat/Km
PMID:20662781. Turnover is about 2.5 min-1.
The enzyme is a flavin monooxygenase by family membership PMID:20662781. The paper did not
measure FAD content directly. UniProt places it in the 3-hydroxybenzoate
6-hydroxylase family, and it has Pfam PF01494 FAD_binding_3.
Substrate range: C7 and C9 HHQ are processed with similar kcat/Km. C5 and C3
analogues are poorer substrates because their Km is higher PMID:20662781.
Oxygen is the limiting substrate in vivo. Anaerobic P. aeruginosa makes no PQS
and has defects in PQS-controlled behaviours such as membrane vesicle
formation. These behaviours recover as soon as O2 returns, without new protein
synthesis PMID:20662781.
Genetics: pqsH is required for PQS synthesis, and its transcription depends on
LasR PMID:12426334. It was originally predicted as a "putative FAD-dependent
monooxygenase" PMID:12426334.
Comparative work: PqsH and the catabolic ortholog AqdB (Mycobacteroides
abscessus) catalyse the same 3-hydroxylation PMID:33452035. AQ 3-monooxygenases do not discriminate AQs from AQNOs, so PqsH
may also make PQS-N-oxide (abstract only; full text not cached).
Localization: no TM segments, but the protein associates with membrane
fractions when overexpressed PMID:20662781. Not strong enough to add a
cellular-component term.

GO term check (OLS / go-basic.obo)

GO:0102164 2-heptyl-3-hydroxy-4(1H)-quinolone synthase activity is_a GO:0016709
(NAD(P)H-dependent, one O incorporated), which is_a GO:0004497 monooxygenase
activity. GO:0102164 is therefore the exact, more specific term for the IDA in
PMID:20662781.
GO has no "quinolone signal biosynthetic process" term (searched OLS and
go-basic.obo), so GO:0044550 secondary metabolite biosynthetic process is the
most specific available BP.
GO:0009372 quorum sensing: the definition includes "producing small, diffusible,
signal molecules", so a signal synthase arguably does part of quorum sensing.
Comparator check: pqsB and pqsC (same pathway, same role) carry only GO:0044550,
not quorum sensing. I did not add a NEW row; raised as a question instead.

PseudoCAP IBA-seed assessment

Tree analysis: pqsH-bioinformatics/RESULTS.md. PTN008173107 is the root of the
PTHR45934 tree. Its children are an Emericella leaf and a horizontal-transfer
node, and under that node sit PqsH, Streptomyces SCO1338 and a 294-leaf
Viridiplantae clade (Arabidopsis MO1/MO2/MO3, CTF2A/B, ...).

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN008173107	GO:0004497 monooxygenase activity	1 (sole seed)	297 (43 taxa)	GO:0004497 monooxygenase activity, IDA, PMID:20662781 (PseudoCAP)	SOUND	The seed is direct evidence: a purified enzyme hydroxylates HHQ with NADH and O2, which meets the monooxygenase definition. The seed is under-specific (the paper supports GO:0102164), but the IBD needs only the generic term. The IBD sits at the family root of class A FAD aromatic hydroxylases (FAD_binding_3/MOase), and generic monooxygenase activity is the right level there. The PqsH-specific GO:0102164 would be wrong on this node, since 294/297 leaves are plant proteins. Caveat: every plant IBA rests on a single bacterial seed on a horizontally transferred branch. No plant member contributed experimental support, and plant catalytic-residue conservation was not checked.

Recommended actions: PseudoCAP could refine the IDA to GO:0102164. This would
not break the IBD, because GO:0102164 is_a GO:0004497 and a descendant term is
valid IBD evidence. I filed no GO_CENTRAL defect: the node term is generic and
plausible. The caveat is listed under suggested_questions.