GATB notes

Deep research

GATB-deep-research-claude-code.md came from just deep-research-claude-code human GATB --timeout 1700.
It ran for 39 s with 2 web searches (web_search_requests: 2) and 4 citations, and states that it did not
read full texts. It also reports, and declined to follow, an injected "REMINDER" instruction in a search
result. It was used only as a list of leads.

Function

• GATB (formerly PET112/PET112L) = GatB subunit of mitochondrial GatCAB (QRSL1-GATB-GATC), GatB/GatE family.
• UniProt (HAMAP MF_03147): GatB recognises tRNA(Gln), phosphorylates the tRNA-bound Glu side chain with ATP
  (gamma-phospho-Glu-tRNA(Gln)) and amidates it with ammonia supplied by GatA; binds 2 Mg2+.
• Human GatCAB identified, knockdown of any subunit accumulates Glu-tRNA(Gln), reconstituted in vitro
  [PMID:19805282, abstract only].
• Friederich 2018 PMID:30283131: GATB patients (family 1) with lethal cardiomyopathy; reduced GatB protein,
  respiratory chain deficiencies in fibroblasts rescued by GATB-V5 transduction; V5-GatB strictly mitochondrial
  in U2OS; yeast pet112 model.
• Mitochondrial import of human PET112 shown in vitro [PMID:9878253, abstract only].

Curation decisions

• GO:0070681 obsolete (QuickGO comment: annotations require review rather than migration). Replaced by
  GO:0019988 charged-tRNA amino acid modification, consistent with GATC and QRSL1 reviews.
• GO:0003824 / GO:0016874 / GO:0016884 are all ancestors of GO:0050567 (checked with OAK ancestors -p i);
  the IEA rows are MODIFYed to GO:0050567.
• Protein binding: QRSL1 rows reflect GatCAB co-membership; LINC01561 (Q8N1V8) rows are from proteome-scale
  binary screens with no functional link. All removed.
• No NEW annotations proposed. A tRNA binding term (GatB is the tRNA-recognition subunit by homology)
  was considered but there is no direct human binding assay.

Mitochondrial translation (GO:0032543) and GO:0070127 (2026-10-30, PR #5739 review round)

• GO:0032543 mitochondrial translation is kept as non-core context, not core, and is no
  longer listed in core_functions. GatCAB transamidates Glu-tRNA(Gln) to Gln-tRNA(Gln); it
  prepares a charged tRNA that translation consumes and performs no step of translation on
  the mitoribosome. The knockdown and patient data (PMID:19805282, PMID:30283131) show that
  GatCAB is necessary for mitochondrial protein synthesis, which is necessity evidence, not
  participation. The earlier justification "in the same sense used for mitochondrial
  aminoacyl-tRNA synthetases" was wrong: none of the human mt-aaRS GOA files checked
  (DARS2, AARS2, EARS2, FARS2, TARS2) carries GO:0032543, and the DARS2 and TARS2 reviews use
  GO:0070127 instead. The MTO1 review likewise does not claim GO:0032543.
• GO:0070127 tRNA aminoacylation for mitochondrial protein translation was considered and
  not added. Its definition is "the synthesis of aminoacyl tRNA by the formation of an ester
  bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA" (go.db). GatCAB
  forms no ester bond: it amidates the side chain of glutamate already esterified to
  tRNA(Gln) by EARS2, so the reaction is a modification of a charged tRNA (GO:0019988), not
  aminoacylation.