np20 / zur (PA5499, Q9HT74) review notes

Literature

Np20 is the P. aeruginosa zinc uptake regulator (Zur): np20 is co-transcribed with znuC and znuB; Δzur cells accumulate more intracellular zinc; znuA transcription is zinc-repressed in PAO1 but not in PAO-Zur PMID:24086521; recombinant Zur binds the znuA promoter, and binding is lost with the zinc chelator TPEN PMID:24086521. Full text cached (PMC3781045).
In a transposon screen for pyocyanin-deficient mutants, an np20 mutant had reduced transcription of several quorum-sensing-controlled genes PMID:12426334; the authors note np20 is a Zur homologue. The mechanism linking Zur to pyocyanin was not examined. Full text cached.
Domain: Fur family (PF01475), PANTHER PTHR33202 (zinc uptake regulation protein); PIRSR zinc-binding site.

Search: PubMed metadata for both GOA-cited PMIDs, both full texts cached and read for the np20 passages. NCBI E-utilities and Europe PMC search were unavailable (HTTP 500/503) during this session.

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?
PTN002112386	GO:0045892 negative regulation of DNA-templated transcription	16	83 (37 taxa)	GO:0045892, IDA, PMID:24086521	SOUND	Full text: zinc-dependent repression of znuA lost in Δzur, plus specific, zinc-dependent EMSA binding to the znuA promoter.	15 others incl. Fur of E. coli (P0A9A9), B. subtilis (P54574), P. aeruginosa (Q03456), Listeria (Q8Y5U9) and M. tuberculosis Zur (P9WN85)	Yes
PTN002112386	GO:1900376 regulation of secondary metabolite biosynthetic process	2	71 (33 taxa)	GO:1900376, IMP, PMID:12426334	INDIRECT-PHENOTYPE	Full text: a pleiotropic transposon-mutant phenotype (less pyocyanin, lower expression of quorum-sensing-controlled genes) with no mechanism shown; Np20's demonstrated function is zinc-responsive repression of zinc uptake genes. PSEUDOCAP defect DELETE_ROW, PROBABLE.	P. aeruginosa Fur (Q03456; PseudoCAP IMP GO:1900705 negative regulation of siderophore biosynthesis, PMID:8885270)	No: it would rest on Fur alone, a Fur-lineage function, while the node is the whole Fur superfamily (Fur, Zur, PerR, Irr and others)

Node-level GO_CENTRAL defect for the GO:1900376 IBD at PTN002112386 is already recorded once, on the GO:1900705 row of genes/PSEAE/fur/fur-ai-review.yaml (WRONG_TERM, CHECK, PROBABLE); it is not duplicated here. Note that the fur defect described the np20 seed as reasonable for that gene; this review finds it an indirect phenotype, which strengthens the case for withdrawing the IBD. The GO:1900376 IBA row on np20 is removed.

The other PTN002112386 IBDs (GO:0045892, GO:0003700, GO:0000976, GO:0008270) rest on many characterised Fur-family repressors and stand (see the fur notes).