GGAT1 (At1g23310, Q9LR30) curation notes

Deep research could not be run in this environment (no provider API keys). These notes are a
literature summary built only from cached publications (publications/PMID_*.md) and the UniProt
record (GGAT1-uniprot.txt). No *-deep-research-*.md file exists for this gene.

Identity and family

• GGAT1 (synonyms AOAT1, GGT1, AlaAT3-like) is one of four alanine aminotransferase (AlaAT)-like
  class I PLP-dependent aminotransferases in Arabidopsis; GGAT1 and GGAT2 (At1g70580) carry a C-terminal
  PTS1 PMID:12529529.
• UniProt: "Belongs to the class-I pyridoxal-phosphate-dependent aminotransferase family. Alanine
  aminotransferase subfamily." PANTHER PTHR11751:SF472.

Activities (substrate breadth)

• Recombinant GGAT1 and GGAT2 catalyse four transaminations PMID:12529529.
• No serine:glyoxylate or aspartate aminotransferase activity PMID:12529529.
• Kinetics (UniProt, from PMID:12529529): Km 0.27 mM glyoxylate, 3 mM glutamate, 7.16 mM alanine,
  0.27 mM 2-oxoglutarate, 0.33 mM pyruvate.
• The AGT (Ala:glyoxylate) reaction was detected but not characterized kinetically, and its
  physiological significance is disputed PMID:12529529.

Judgement: the glutamate:glyoxylate reaction (GO:0047958, glycine:2-oxoglutarate transaminase,
written in the reverse direction) is the core photorespiratory activity. Ala:2-oxoglutarate (GO:0004021)
and Ala:glyoxylate (GO:0008453) are genuine but non-core.

Localization

• Peroxisome: GFP fusion in BY-2 cells depends on PTS1 PMID:12631323; sucrose-gradient fractionation PMID:12529529; leaf peroxisome proteomics PMID:17951448.
• Proteomic hits in vacuole, chloroplast, apoplast, nucleus/membrane fractions and crude cytosol are
  best explained as contamination by an abundant peroxisomal matrix enzyme.

Physiological role

• The aoat1-1 (ggat1) knockout has drastically reduced leaf GGAT activity and a conditional,
  high-CO2-rescued growth phenotype [PMID:12631323 "The activity of GGAT and alanine:glyoxylate
  aminotransferase (AGAT) in the above-ground tissues of aoat1-1 was reduced drastically"; "These
  phenotypes resembled those of photorespiration-deficient mutants."].
• Phenotype is weak because GGAT2 provides residual activity PMID:22303256.
• Overexpression raises Ser, Gly and citrulline in light, repressed by high CO2 PMID:16950862.
• Expression in roots suggests non-photorespiratory roles PMID:16950862.
• ggt1 mutants were recovered in an ABA/RD29A:LUC screen; altered H2O2, ABA and proline
  PMID:17318317. Treated as an indirect consequence
  of photorespiratory impairment.

Annotation-specific notes

• Hypoxia IEP (PMID:17319845, abstract only): the paper is about AlaAT1/AlaAT2; UniProt cites it for slight
  low-oxygen induction of GGAT1 in shoots. Kept as non-core expression response.
• L-alanine catabolic process (UniPathway IEA): the hypoxia alanine breakdown role belongs to AlaAT1
  PMID:17319845; no evidence that
  peroxisomal GGAT1 catabolizes alanine in vivo, so marked over-annotated.
• mRNA binding: GGAT was a hit in a leaf RNA interactome capture screen (PMID:32344669) with no follow-up;
  a peroxisomal matrix enzyme, so marked over-annotated.

Module comparison (modules/photorespiration_c2_cycle.yaml, ggat_step)

Module asserts GO:0047958 / GO:0009853 / GO:0005777 for GGAT1. This review agrees on all three.