GDCST (At1g11860; synonym GDT1) encodes the T protein (aminomethyltransferase, EC 2.1.2.10) of the mitochondrial glycine cleavage system, also called the glycine decarboxylase complex, and is the only T-protein gene in Arabidopsis. The nuclear-encoded precursor carries an N-terminal mitochondrial transit peptide, and the mature GcvT-family enzyme acts in the mitochondrial matrix with the P, H and L proteins. After the P protein decarboxylates glycine and loads the aminomethyl group onto the lipoyl arm of the H protein, the T protein releases ammonia and transfers the one-carbon unit to tetrahydrofolate, forming 5,10-methylenetetrahydrofolate and leaving the H-protein lipoyl arm reduced. Mitochondrial serine hydroxymethyltransferase (SHM1) then uses this 5,10-methylenetetrahydrofolate to convert a second glycine to serine. Together the two enzymes make up the mitochondrial part of the photorespiratory C2 cycle, and they also supply one-carbon units. T protein is far more abundant in leaves than the other glycine cleavage proteins. Plants with about 5% of normal T protein grow in air with only moderate glycine accumulation, but knockout plants die even in CO2-enriched air. This shows that the enzyme is essential beyond photorespiration, most likely for one-carbon metabolism.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003729 mRNA binding | IDA PMID:32344669 Discovering the RNA-Binding Proteome of Plant Leaves with an... | KEEP AS NON CORE | Summary: GDCST was recovered in a proteome-wide leaf RNA interactome capture screen that also recovered many metabolic and photosynthetic enzymes lacking canonical RNA-binding domains. Reason: The in vivo crosslinking capture is experimental evidence for RNA association, but it is a high-throughput screen whose physiological significance for a mitochondrial matrix aminomethyltransferase is unknown. It is retained as non-core and does not describe the enzyme's established role. Supporting Evidence: PMID:32344669 a large proportion of leaf RBPs lack known RNA-binding domains, suggesting unconventional modes of RNA binding |
| GO:0004047 aminomethyltransferase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Aminomethyltransferase (T-protein) activity, propagated from an ancestral GcvT node that is seeded by characterized bacterial, yeast and human T proteins. Reason: This is the defining catalytic activity of the glycine cleavage T protein. GDCST is a full-length GcvT-family protein (TIGR00528, PANTHER PTHR43757:SF2) that conserves the substrate-binding residues, and the Arabidopsis literature identifies it as the T protein of the glycine decarboxylase complex. Nothing suggests divergence from the ancestral function. Supporting Evidence: PMID:22303256 The amino methylene group bound to the H-protein is further metabolized by the monomeric aminomethyltransferase T-protein (EC 2.1.2.10) PMID:28866761 T-protein is the aminomethyltransferase of the glycine cleavage multienzyme system (GCS), also known as the glycine decarboxylase complex file:ARATH/GDCST/GDCST-uniprot.txt SIMILARITY: Belongs to the GcvT family. |
| GO:0004047 aminomethyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Aminomethyltransferase activity inferred from the GcvT InterPro signature and the EC 2.1.2.10 / RHEA:16945 mapping. Reason: Consistent with the IBA row and the literature. The IPR006223 GcvT signature is specific to glycine cleavage T proteins. Supporting Evidence: PMID:22303256 During this reaction, NH 3 is released and a methylene group is transferred to tetrahydrofolate resulting in the formation of 5,10-methylene tetrahydrofolate (CH 2 -THF) |
| GO:0005576 extracellular region | HDA PMID:28887381 Global Analysis of Membrane-associated Protein Oligomerizati... | MARK AS OVER ANNOTATED | Summary: Extracellular-region assignment from a membrane-associated protein correlation-profiling dataset. Reason: GDCST has a mitochondrial transit peptide and acts in the mitochondrial matrix as part of the glycine cleavage system. Detecting an abundant leaf mitochondrial enzyme in a fractionation-based proteomics dataset does not establish secretion. The call most likely reflects carry-over during fractionation. Supporting Evidence: file:ARATH/GDCST/GDCST-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion |
| GO:0005739 mitochondrion | HDA PMID:18385124 Heterogeneity of the mitochondrial proteome for photosynthet... | ACCEPT | Summary: Detected in the mitochondrial proteome of photosynthetic shoots. Reason: Consistent with the transit peptide and with the mitochondrial location of the glycine decarboxylase complex. This study specifically noted the photorespiratory machinery in shoot mitochondria. Supporting Evidence: PMID:18385124 showed the elevated level of the photorespiratory apparatus and its complex interplay with glycolate, cysteine, formate, and one-carbon metabolism |
| GO:0005739 mitochondrion | HDA PMID:25293756 A proteomic strategy for global analysis of plant protein co... | ACCEPT | Summary: Assigned to mitochondrion in a leaf protein-complex proteomics study. Reason: Consistent with all other localization evidence for the T protein. Supporting Evidence: PMID:22303256 The combined reaction of glycine decarboxylase (GLD) and serine hydroxymethyltransferase (SHM) represents the mitochondrial part of the major photorespiratory pathway. |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: Mitochondrial activity location inherited from the eukaryotic mitochondrial T-protein node. GDCST is one of the seed genes. Reason: The eukaryotic T proteins of this clade are mitochondrial matrix enzymes. GDCST's own experimental mitochondrial annotation is one of the descendant evidences for this node, which is expected and not circular. Supporting Evidence: file:ARATH/GDCST/GDCST-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion |
| GO:0005739 mitochondrion | IDA PMID:28866761 T-protein is present in large excess over the other proteins... | ACCEPT | Summary: Mitochondrial location assigned by the curator from the Timm et al. T-protein study. Only the abstract is cached. Reason: The full text is not available here, but a mitochondrial location fits the transit peptide, the proteomics data and the known matrix location of the glycine cleavage system. We defer to the curator. Supporting Evidence: PMID:28866761 T-protein is the aminomethyltransferase of the glycine cleavage multienzyme system (GCS), also known as the glycine decarboxylase complex |
| GO:0005739 mitochondrion | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic mitochondrion annotation from the UniProt subcellular-location mapping. Reason: Consistent with the experimental and phylogenetic evidence. Supporting Evidence: file:ARATH/GDCST/GDCST-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion |
| GO:0005739 mitochondrion | ISM GO_REF:0000122 | ACCEPT | Summary: Mitochondrial targeting predicted by AtSubP sequence analysis. Reason: The prediction agrees with the experimental evidence. Supporting Evidence: file:ARATH/GDCST/GDCST-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion |
| GO:0005960 glycine cleavage complex | IEA GO_REF:0000002 | ACCEPT | Summary: Membership of the glycine cleavage complex, inferred from the GcvT InterPro signature. Reason: GDCST is the T protein of the Arabidopsis glycine decarboxylase complex, which consists of the P, H, T and L proteins. Supporting Evidence: PMID:22303256 In Arabidopsis, the four proteins are encoded by eight genes, two genes each for P-protein (At4g33010 and At2g26080) and L-protein (At3g17240 and At1g48030), three genes for H-protein (At2g35370, At2g35120 and At1g32470) and one gene for T-protein (At1g11860) file:ARATH/GDCST/GDCST-uniprot.txt SUBUNIT: The glycine cleavage system is composed of four proteins: P, T, L and H. |
| GO:0006546 glycine catabolic process | IEA GO_REF:0000002 | ACCEPT | Summary: Glycine catabolic process, inferred from the GcvT InterPro signature. Reason: This is a correct parent of the more specific GO:0019464 (glycine decarboxylation via glycine cleavage system), which is accepted below. The glycine cleavage system is the major route of glycine catabolism in plant mitochondria, so the broader term still carries meaning. Supporting Evidence: PMID:22303256 Glycine is decarboxylated and deaminated by the multienzyme complex glycine decarboxylase yielding CO 2 , NH 3 , NADH and 5, 10-methylenetetrahydrofolate. |
| GO:0009507 chloroplast | HDA PMID:18431481 Sorting signals, N-terminal modifications and abundance of t... | MARK AS OVER ANNOTATED | Summary: Detected in a large-scale proteome of isolated chloroplasts. Reason: GDCST has a mitochondrial transit peptide and is a component of the mitochondrial glycine decarboxylase complex. No targeted study supports a plastid pool. The authors of this dataset estimate that several hundred of their identifications are non-chloroplast contaminants, so the detection most likely reflects mitochondrial carry-over of this abundant leaf protein. Supporting Evidence: PMID:18431481 from manual evaluation we estimate that 300–350 proteins likely represent false positive identifications and/or non-chloroplast contaminations |
| GO:0009534 chloroplast thylakoid | HDA PMID:20061580 AT_CHLORO, a comprehensive chloroplast proteome database wit... | MARK AS OVER ANNOTATED | Summary: Assigned to the thylakoid subfraction in the AT_CHLORO chloroplast proteome database. Reason: A mitochondrial matrix enzyme with a mitochondrial transit peptide. Detection in a chloroplast subfraction is most likely contamination and is not supported by any targeted localization study. Supporting Evidence: PMID:18431481 from manual evaluation we estimate that 300–350 proteins likely represent false positive identifications and/or non-chloroplast contaminations |
| GO:0009570 chloroplast stroma | HDA PMID:20061580 AT_CHLORO, a comprehensive chloroplast proteome database wit... | MARK AS OVER ANNOTATED | Summary: Assigned to the stroma subfraction in the AT_CHLORO chloroplast proteome database. Reason: As for the other chloroplast proteome hits, this most likely reflects co-purifying mitochondrial material. The soluble glycine decarboxylase subunits are among the most abundant leaf mitochondrial proteins. Supporting Evidence: PMID:18431481 from manual evaluation we estimate that 300–350 proteins likely represent false positive identifications and/or non-chloroplast contaminations |
| GO:0009941 chloroplast envelope | HDA PMID:12938931 Proteomic study of the Arabidopsis thaliana chloroplastic en... | MARK AS OVER ANNOTATED | Summary: Detected in a proteome of mixed chloroplast envelope membranes. Reason: A soluble mitochondrial matrix enzyme is unlikely to be a chloroplast envelope protein. The detection most likely reflects contamination of the envelope preparation. Supporting Evidence: file:ARATH/GDCST/GDCST-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion |
| GO:0019464 glycine decarboxylation via glycine cleavage system | IBA GO_REF:0000033 | ACCEPT | Summary: Participation in glycine decarboxylation via the glycine cleavage system, inherited from the mitochondrial T-protein node. Reason: The T protein catalyses an obligatory step of the glycine cleavage cycle, the transfer of the aminomethyl unit from lipoyl-H protein to tetrahydrofolate with release of ammonia. This is the core process for GDCST and matches the T-protein role in the glycine cleavage system module. Supporting Evidence: PMID:22303256 The amino methylene group bound to the H-protein is further metabolized by the monomeric aminomethyltransferase T-protein (EC 2.1.2.10) PMID:28866761 T-protein is the aminomethyltransferase of the glycine cleavage multienzyme system (GCS), also known as the glycine decarboxylase complex |
| GO:0022626 cytosolic ribosome | HDA PMID:15821981 High heterogeneity within the ribosomal proteins of the Arab... | MARK AS OVER ANNOTATED | Summary: Co-migrated with cytoplasmic 80S ribosomes in a ribosome proteomics study. Reason: The authors describe co-migrating non-ribosomal proteins as possible associations only. A mitochondrial matrix enzyme has no established role at the cytosolic ribosome, so the hit most likely reflects co-sedimentation of a large complex. Supporting Evidence: PMID:15821981 we have identified a number of non-ribosomal proteins that co-migrate with the plant 80S ribosomes during gradient centrifugation |
| GO:0048046 apoplast | HDA PMID:18538804 Hydroponic isotope labelling of entire plants (HILEP) for qu... | MARK AS OVER ANNOTATED | Summary: Apoplast assignment from a whole-plant quantitative proteomics (HILEP) study. Reason: The study is a method paper on whole-plant protein extracts (abstract only) and gives no specific evidence for secretion. GDCST is a mitochondrial matrix enzyme with a mitochondrial transit peptide. Supporting Evidence: file:ARATH/GDCST/GDCST-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion |
| GO:0009853 photorespiration | IMP PMID:28866761 T-protein is present in large excess over the other proteins... | NEW | Summary: The glycine cleavage T protein catalyses a step of the photorespiratory conversion of glycine to serine in leaf mitochondria. A T-protein knockdown accumulates glycine in air. Reason: Participation test: GDCST does work in the pathway, because it catalyses the aminomethyl transfer that produces the 5,10-methylene-THF used by SHM1 in the photorespiratory glycine-to-serine conversion. It is not merely required for the pathway. Comparator check: the other enzymes of the C2 cycle that catalyse a step (SHM1, GGAT1, AGT1, HPR, GLYK) all carry GO:0009853 in GOA. The glycine decarboxylase subunits have no photorespiration annotation, but no convention excludes catalytic subunits, so this absence looks like a curation gap. The knockdown phenotype (glycine accumulation, delayed growth in air) is consistent. Knockout lethality at high CO2 shows a further essential non-photorespiratory role in one-carbon metabolism. Supporting Evidence: PMID:28866761 T-protein is the aminomethyltransferase of the glycine cleavage multienzyme system (GCS), also known as the glycine decarboxylase complex, and essential for photorespiration and one-carbon metabolism PMID:28866761 displayed only some minor changes, such as a moderate glycine accumulation in combination with somewhat delayed growth PMID:22303256 The combined reaction of glycine decarboxylase (GLD) and serine hydroxymethyltransferase (SHM) represents the mitochondrial part of the major photorespiratory pathway. |
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Download this section (compressed HTML)Q: Why is GDCST knockout lethal even in CO2-enriched air when a knockdown with about 5% residual T protein grows almost normally in air? Which one-carbon sinks (for example in vascular tissue) depend on glycine cleavage-derived 5,10-methylene-THF?
Q: GDCST, GLDP1/2, GDCH and the mitochondrial LPDs lack photorespiration (GO:0009853) annotations in GOA, but SHM1 and the other C2-cycle enzymes have them. Should the GDC catalytic subunits be annotated to photorespiration consistently?
Experiment: Tissue-specific complementation of the lethal gdcst knockout, using a mesophyll-specific promoter versus a vascular promoter, to separate the photorespiratory and non-photorespiratory requirements for T protein.
Type: genetic complementation
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