GDCST (At1g11860, UniProt O65396) - curation notes

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These notes are a manual literature summary built only from the cached
publications in publications/, the UniProt record (GDCST-uniprot.txt) and
PubMed searches. No -deep-research-*.md file exists for this gene.

Identity

• UniProt O65396 (GCST_ARATH), "Aminomethyltransferase, mitochondrial", EC 2.1.2.10,
  AltName "Glycine cleavage system T protein"; gene GDCST, synonym GDT1, locus At1g11860.
• Predicted N-terminal mitochondrial transit peptide (residues 1-24, ECO:0000255).
• Family: GcvT family (InterPro IPR006223 GcvT; NCBIfam TIGR00528 gcvT;
  PANTHER PTHR43757:SF2 "AMINOMETHYLTRANSFERASE, MITOCHONDRIAL").
• Single-copy gene in Arabidopsis
  PMID:22303256.

Biochemical function

• T-protein is the aminomethyltransferase of the glycine cleavage system (GCS;
  glycine decarboxylase complex, GDC): it accepts the aminomethyl group carried on
  the lipoyl arm of H-protein, releases NH3, and transfers the methylene unit to
  tetrahydrofolate (THF) forming 5,10-methylene-THF
  PMID:22303256
  PMID:22303256.
• UniProt catalytic activity: RHEA:16945 (aminomethyl-dihydrolipoyl-[protein] + THF =
  dihydrolipoyl-[protein] + 5,10-methylene-THF + NH4+); this is annotated by
  similarity (no Arabidopsis-specific kinetic data in the cache).
• The GDC is composed of four proteins, P, T, L and H (UniProt SUBUNIT).
  In pea the complex stoichiometry was 4P:27H:9T:2L
  PMID:22303256.

Physiological role

• GDC + mitochondrial SHMT form the mitochondrial part of the photorespiratory C2
  cycle PMID:22303256.
• Timm et al. 2018 (abstract only in cache): T-protein is essential for
  photorespiration and one-carbon metabolism; knockout is lethal even in 1% CO2,
  whereas a knockdown with ~5% residual T-protein survives in air with moderate
  glycine accumulation; overexpression (up to 3x) has no effect on photosynthesis
  or growth; T-protein is in large excess over the other GCS proteins
  PMID:28866761
  PMID:28866761
  PMID:28866761.
• The lethality at high CO2 indicates the non-photorespiratory (one-carbon supply)
  role of GCS is essential; this matches GLDP1/GLDP2 double mutants (see the C2
  cycle module).
• T-protein knockdown (gldt1) has been used as a genetic background for
  photorespiration studies PMID:38518065.

Localization

• Mitochondrion (matrix enzyme; predicted transit peptide). Repeated detection in
  mitochondrial proteomes (PMID:18385124, PMID:25293756) and IDA (PMID:28866761,
  curator-assigned; full text not cached).
• Detections in chloroplast (PMID:18431481, PMID:20061580, PMID:12938931),
  cytosolic ribosome (PMID:15821981), apoplast (PMID:18538804) and extracellular
  region (PMID:28887381) proteomes are most consistent with carry-over of an
  abundant leaf mitochondrial protein. The chloroplast proteome authors themselves
  estimate many non-plastid contaminants
  PMID:18431481.
  The 80S ribosome study reports co-migrating non-ribosomal proteins
  PMID:15821981.

Other annotations

• mRNA binding (IDA, PMID:32344669): from a leaf RNA interactome capture screen,
  which found many metabolic/photosynthetic proteins without canonical RBDs
  PMID:32344669.
  Physiological relevance unknown.

Curation decisions summary

• Core: GO:0004047 aminomethyltransferase activity; GO:0019464 glycine
  decarboxylation via glycine cleavage system; part of GO:0005960 glycine cleavage
  complex; located in mitochondrion.
• NEW: GO:0009853 photorespiration (IMP, PMID:28866761). T-protein catalyses a
  step of the photorespiratory glycine-to-serine conversion (participation test
  passed: it performs the aminomethyl transfer). Comparator check: the other
  C2-cycle enzymes reviewed in this repository (SHM1, GGAT1, AGT1, HPR, GLYK) carry
  GO:0009853 in GOA; the GDC subunits (GLDP1, GLDP2, GDCH, GDCST) do not, which
  looks like a curation gap rather than a convention, because the GDC subunits
  catalyse photorespiratory steps just like SHM1 does.
• Proteome-only non-mitochondrial locations marked as over-annotations.

Module cross-check

• modules/glycine_cleavage_system.yaml T-protein role: GO:0004047, family
  PANTHER PTHR43757:SF2 (the same subfamily as GDCST in UniProt), process
  GO:0019464. Consistent with this review.
• modules/photorespiration_c2_cycle.yaml lists GDCST (O65396) as the
  Arabidopsis T protein. Consistent.