Shmt (CG3011) encodes the single Drosophila serine hydroxymethyltransferase (EC 2.1.2.1), a pyridoxal 5'-phosphate-dependent tetrameric enzyme that reversibly converts L-serine and tetrahydrofolate into glycine and 5,10-methylene-tetrahydrofolate, supplying one-carbon units for purine, thymidylate and methionine/S-adenosylmethionine synthesis. Alternative transcripts encode a long isoform with an N-terminal mitochondrial presequence and a shorter cytoplasmic isoform, so the one gene covers the mitochondrial and cytosolic functions split between SHMT2 and SHMT1 in vertebrates; a minor nuclear pool associates with the nuclear lamina. Maternal Shmt catalytic activity is essential for the last syncytial nuclear cycle before the midblastula transition, and glycine synthesis in circadian pacemaker neurons contributes to normal free-running period.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004372 glycine hydroxymethyltransferase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Core SHMT activity inherited from the PANTHER SHMT ancestral node, which includes the fly gene among its experimentally supported descendants. Reason: Fly genetic data show the catalytic activity is required, and the protein is a canonical eukaryotic SHMT. Supporting Evidence: PMID:28515048 A transgene with this allele did not complement SHMT[X238], indicating that the enzymatic function is required. PMID:28515048 The evolutionarily highly conserved SHMT is a pyridoxal phosphate-containing enzyme that converts serine into glycine and vice versa (Figure 1). |
| GO:0004372 glycine hydroxymethyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: EC 2.1.2.1 / InterPro SHMT mapping to the core activity. Reason: Specific family signature consistent with experimental data. Supporting Evidence: file:DROME/Shmt/Shmt-uniprot.txt EC=2.1.2.1 PMID:28515048 The evolutionarily highly conserved SHMT is a pyridoxal phosphate-containing enzyme that converts serine into glycine and vice versa (Figure 1). |
| GO:0004372 glycine hydroxymethyltransferase activity | IMP PMID:28515048 Essential Function of the Serine Hydroxymethyl Transferase (... | ACCEPT | Summary: A catalytic-center point mutant (E130Q) fails to rescue the null allele, whereas E. coli SHMT rescues, showing that the enzymatic activity is required. Reason: Direct fly evidence that the biological function depends on SHMT catalysis; catalytic activity itself is well established for the family. Supporting Evidence: PMID:28515048 A transgene with this allele did not complement SHMT[X238], indicating that the enzymatic function is required. |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: Nuclear pool inherited from the ancestral node that includes SHMT1 orthologs with nuclear localization. Reason: Consistent with the fly IDA showing a detergent-resistant nucleoplasmic pool; nuclear SHMT supports de novo thymidylate synthesis in vertebrates. Supporting Evidence: PMID:28515048 Staining of such extracted cells revealed a nucleoplasmic staining for SHMT together with the lamina protein LaminDm0 (Figure 3D). |
| GO:0005634 nucleus | IDA PMID:28515048 Essential Function of the Serine Hydroxymethyl Transferase (... | ACCEPT | Summary: Detergent-extracted S2 cells show a minor nucleoplasmic SHMT pool colocalizing with lamin. Reason: Direct immunostaining evidence for a nuclear pool. Supporting Evidence: PMID:28515048 Staining of such extracted cells revealed a nucleoplasmic staining for SHMT together with the lamina protein LaminDm0 (Figure 3D). |
| GO:0005737 cytoplasm | IDA PMID:28515048 Essential Function of the Serine Hydroxymethyl Transferase (... | ACCEPT | Summary: SHMT shows uniform cytoplasmic staining in embryos. Reason: Direct immunostaining; the shorter isoform lacking the presequence is cytoplasmic. Supporting Evidence: PMID:28515048 In wild-type embryos, we detected uniform cytoplasmic staining during blastoderm stages (Figure 3C) and in later developmental stages. |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: Mitochondrial pool inherited from the SHMT2-type ancestral node. Reason: The single fly gene encodes a long isoform with an N-terminal mitochondrial presequence in addition to the cytoplasmic form, so it covers both compartments. Supporting Evidence: PMID:28515048 a longer one of 470 amino acid residues with a putative N-terminal mitochondrial presequence, and a shorter one of 400 amino acid residues PMID:28515048 SHMT is present in mitochondria and the cytoplasm. |
| GO:0005759 mitochondrial matrix | ISS GO_REF:0000024 | ACCEPT | Summary: Mitochondrial matrix transferred from human SHMT2. Reason: The presequence-bearing isoform is expected to be imported into the matrix, where mitochondrial one-carbon metabolism takes place. Supporting Evidence: PMID:28515048 a longer one of 470 amino acid residues with a putative N-terminal mitochondrial presequence, and a shorter one of 400 amino acid residues |
| GO:0006545 glycine biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: Glycine production from serine inherited from the SHMT ancestral node. Reason: SHMT directly catalyzes the serine-to-glycine conversion. Supporting Evidence: PMID:28515048 The evolutionarily highly conserved SHMT is a pyridoxal phosphate-containing enzyme that converts serine into glycine and vice versa (Figure 1). |
| GO:0006545 glycine biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: InterPro/ARBA mapping to glycine biosynthesis. Reason: Same as above; the catalytic step itself forms glycine. Supporting Evidence: PMID:28515048 The evolutionarily highly conserved SHMT is a pyridoxal phosphate-containing enzyme that converts serine into glycine and vice versa (Figure 1). |
| GO:0006545 glycine biosynthetic process | IMP PMID:28515048 Essential Function of the Serine Hydroxymethyl Transferase (... | ACCEPT | Summary: Genetic evidence that SHMT enzymatic function is essential at the midblastula transition. Reason: The curator inferred glycine/serine interconversion from the catalytic-mutant and rescue data; SHMT performs the glycine-forming step. Supporting Evidence: PMID:28515048 A transgene with this allele did not complement SHMT[X238], indicating that the enzymatic function is required. PMID:28515048 The evolutionarily highly conserved SHMT is a pyridoxal phosphate-containing enzyme that converts serine into glycine and vice versa (Figure 1). |
| GO:0006565 L-serine catabolic process | IMP PMID:28515048 Essential Function of the Serine Hydroxymethyl Transferase (... | ACCEPT | Summary: SHMT consumes serine in the forward reaction. Reason: Serine cleavage to glycine and a methylene-THF one-carbon unit is the canonical direction feeding C1 metabolism; supported by the catalytic-mutant data. Supporting Evidence: PMID:28515048 The evolutionarily highly conserved SHMT is a pyridoxal phosphate-containing enzyme that converts serine into glycine and vice versa (Figure 1). PMID:28515048 The released hydroxymethyl (C1) unit is transferred to THF to give rise to N5, N10 methylene THF. |
| GO:0030170 pyridoxal phosphate binding | IBA GO_REF:0000033 | ACCEPT | Summary: PLP cofactor binding inherited from the SHMT family. Reason: SHMT is a PLP-dependent fold-type I enzyme; a genuine but subsidiary property. Supporting Evidence: PMID:28515048 The evolutionarily highly conserved SHMT is a pyridoxal phosphate-containing enzyme that converts serine into glycine and vice versa (Figure 1). |
| GO:0030170 pyridoxal phosphate binding | IEA GO_REF:0000002 | ACCEPT | Summary: PLP binding from InterPro SHMT PLP-binding site signature. Reason: Same as above. Supporting Evidence: file:DROME/Shmt/Shmt-uniprot.txt Name=pyridoxal 5'-phosphate |
| GO:0035999 folate cycle | IEA GO_REF:0000120 | ACCEPT | Summary: SHMT generates 5,10-methylene-THF, feeding the folate cycle. Reason: Direct participant in the folate (one-carbon) cycle. Supporting Evidence: PMID:28515048 The released hydroxymethyl (C1) unit is transferred to THF to give rise to N5, N10 methylene THF. |
| GO:0042752 regulation of circadian rhythm | IMP PMID:28380364 Organization of Circadian Behavior Relies on Glycinergic Tra... | KEEP AS NON CORE | Summary: Knockdown of glycine synthesis in LNv clock neurons lengthens the free-running period, implicating glycine as a clock-neuron transmitter. Reason: The phenotype reflects SHMT supplying the glycine neurotransmitter pool rather than SHMT acting on clock machinery; it is a legitimate experimental observation but downstream of the core metabolic role. Supporting Evidence: PMID:28380364 impairment of glycine synthesis in LNv neurons increased period length |
| GO:0045329 carnitine biosynthetic process | IC GO_REF:0000111 | KEEP AS NON CORE | Summary: Carnitine biosynthesis inferred from the putative hydroxytrimethyllysine aldolase activity of mammalian SHMT1. Reason: Mammalian SHMT can cleave 3-hydroxy-N6-trimethyllysine in vitro, and the IC is a reasonable chain from that ISS, but there is no insect evidence that SHMT is the physiological aldolase in carnitine synthesis; this is at most a side activity. Supporting Evidence: PMID:28515048 The evolutionarily highly conserved SHMT is a pyridoxal phosphate-containing enzyme that converts serine into glycine and vice versa (Figure 1). |
| GO:0046653 tetrahydrofolate metabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: THF metabolism inherited from the SHMT ancestral node. Reason: SHMT transfers the hydroxymethyl group to THF, forming 5,10-methylene-THF. Supporting Evidence: PMID:28515048 The released hydroxymethyl (C1) unit is transferred to THF to give rise to N5, N10 methylene THF. |
| GO:0046653 tetrahydrofolate metabolic process | IMP PMID:28515048 Essential Function of the Serine Hydroxymethyl Transferase (... | ACCEPT | Summary: Mutant embryos arrest in interphase 13, interpreted as exhaustion of maternally supplied SHMT-dependent C1 metabolites. Reason: Experimentally grounded in the requirement for catalytic activity; SHMT directly produces methylene-THF. Supporting Evidence: PMID:28515048 The released hydroxymethyl (C1) unit is transferred to THF to give rise to N5, N10 methylene THF. PMID:28515048 A transgene with this allele did not complement SHMT[X238], indicating that the enzymatic function is required. |
| GO:0120567 hydroxytrimethyllysine aldolase activity | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Hydroxytrimethyllysine aldolase transferred from human SHMT1. Reason: A side activity of mammalian cytosolic SHMT shown in vitro; plausible for the fly cytoplasmic isoform but not its core role and not tested in flies. Supporting Evidence: file:DROME/Shmt/Shmt-uniprot.txt EC=2.1.2.1 |
Loading supporting content…
Download this section (compressed HTML)Q: Which SHMT-dependent metabolite (thymidylate, purines or S-adenosylmethionine) becomes limiting in interphase 13 of Shmt germline-clone embryos?
Q: Do the mitochondrial and cytoplasmic Shmt isoforms have separable developmental requirements, given that flies have only one SHMT gene?
Experiment: Inject Shmt germline-clone embryos with thymidine, formate or hypoxanthine and score progression through mitosis 13 and cellularization, combined with targeted nucleotide metabolomics.
Hypothesis: Thymidylate (dTMP) depletion causes the interphase-13 arrest of Shmt mutant embryos.
Experiment: Rescue Shmt nulls with genomic transgenes in which the alternative start codons are mutated to express only the long (mitochondrial) or short (cytoplasmic) isoform.
Hypothesis: Mitochondrial and cytoplasmic Shmt isoforms are each sufficient for embryonic viability.
Loading supporting content…
Download this section (compressed HTML)Serine hydroxymethyl transferase (Shmt) encodes a conserved pyridoxal phosphate-containing enzyme that converts serine into glycine and N5,N10-methylentetrahydrofolate. This reaction represents a major source for activated C1 units and tetrahydrofolate-mediated C1 metabolism. Shmt is also predicted to catalyze the cleavage of 3-hydroxy-trimethyllysine into 4-(trimethylamino)butanal and glycine, the second step of carnitine biosynthesis.
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)