gtpbp3 (Danio rerio) review notes

Batch 05 curation notes

• Core interpretation: gtpbp3 encodes a mitochondrial GTPase subunit of the GTPBP3-MTO1 complex required for taurine-containing wobble uridine modification of mitochondrial tRNAs. The core function is GTPase-supported mitochondrial tRNA wobble uridine modification; reduced mitochondrial tRNA aminoacylation phenotypes are treated as downstream consequences rather than direct aminoacyl-tRNA ligase activity.
• Key UniProt support: GTPase component of the GTPBP3-MTO1 complex.
• Existing GOA annotations were reviewed against this core role; broad, inferred, or downstream phenotype annotations were kept as non-core unless they overstate the direct function.

Re-review 2026-09-29

• Rewrote all 23 review blocks (templated reasons replaced; deep-research quotes dropped except one corroborating line). Resolved the PENDING duplicate embryonic organ development IMP (second morpholino) as KEEP_AS_NON_CORE like its twin.
• The six IMP aminoacylation rows (GO:0070143, GO:0070153, GO:0070154, GO:0070155, GO:0070183, GO:0070184) were re-adjudicated MARK_AS_OVER_ANNOTATED -> REMOVE. QuickGO confirms all six terms are obsolete with no replacement, the yaml labels were updated to GOA's "obsolete ..." labels, and the full text shows the knock-out effect runs opposite to a "required for" reading and is indirect: [PMID:30916346 "Strikingly, gtpbp3 knock-out zebrafish displayed the global increases in the aminoacylated efficiencies of mitochondrial tRNAs."; "These data validated that the inactivation of Gtpbp3 changed the conformation of mitochondrial tRNAs."]. Aminoacylation is done by the mt-aaRSs; the observation is already captured by the accepted GO:0070900 IMP from the same paper.
• GO:0030488 tRNA methylation (IBA, PTN000182687 seeded by E. coli MnmE) KEEP_AS_NON_CORE -> MODIFY to GO:0070899 with a propagation_review: the GTPBP3-MTO1 product is taurinomethyl-U34, not a methylated base PMID:30916346. GO:0006400 tRNA modification (IEA) KEEP_AS_NON_CORE -> MODIFY to GO:0070899.
• GO:0005737 cytoplasm (IBA) REMOVE -> KEEP_AS_NON_CORE with propagation_review (NO_FAILURE_NON_CORE): mitochondrion is part_of cytoplasm and the family node includes bacterial MnmE; the informative term is mitochondrion, supported by PMID:27184967 and the UniProt transit peptide. GO:0005525 GTP binding ACCEPT -> KEEP_AS_NON_CORE (entailed by GTPase activity). GO:0036416 tRNA stabilization stays KEEP_AS_NON_CORE on PMID:30916346.
• Localization rows now quote the SUBCELLULAR LOCATION line and the zebrafish isoform localisation instead of the FUNCTION line. Added reference_review and findings for both PMIDs (PMID:27184967 is abstract-only), a standalone description, two questions and one experiment. Validation: 0 errors, 0 warnings.