sptl-1 (C23H3.4) encodes the single C. elegans LCB1/SPTLC1-type subunit of serine palmitoyltransferase (SPT), the enzyme that catalyses the first committed step of de novo sphingolipid biosynthesis, the pyridoxal 5'-phosphate (PLP)-dependent condensation of L-serine with an acyl-CoA to give a 3-ketosphinganine long-chain base. By homology, the active enzyme is a heterodimer of SPTL-1 with one of the LCB2/SPTLC2-type subunits SPTL-2 or SPTL-3, which carry the PLP-binding lysine; SPTL-1 is a class-II PLP-dependent aminotransferase-fold protein that lacks this lysine (Asn at the equivalent position) and, like its orthologs, is expected to sit in the endoplasmic reticulum. In C. elegans the major sphingoid base is the C17 iso-branched d17iso-sphingosine (id17:1), made from a monomethyl branched-chain fatty acyl-CoA, and sptl-1 knockdown lowers nearly all ceramide, glucosylceramide and sphingomyelin species. Loss of sptl-1 causes larval arrest and lethality and a striking conversion of intestinal apicobasal polarity (ectopic lateral lumens), attributed to loss of glycosphingolipids needed for apical membrane biogenesis; a CRISPR model of the human HSAN1 SPTLC1 C133W mutation (SPTL-1 C121W) reproduces these defects and causes neuronal polarity defects. Loss of sptl-1 also suppresses sphingosine accumulation and lysosomal damage in sphingosine kinase (sphk-1) mutants.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004758 serine C-palmitoyltransferase activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT propagation of serine C-palmitoyltransferase activity from the LCB1/SPTLC1 clade (mouse Sptlc1, yeast LCB1, Aspergillus LCB1) to C. elegans SPTL-1. Reason: SPTL-1 sits inside the SPTLC1/LCB1 clade (50% identity to human SPTLC1 vs 30% to SPTLC2 in our alignment), so the IBD node placement covers it. Like other LCB1 subunits SPTL-1 lacks the PLP Schiff-base lysine (Asn297 at the SPTLC2 K379 position), so it is the non-catalytic but obligate partner of the heterodimeric enzyme; GO convention (human SPTLC1, yeast LCB1) annotates this subunit to the activity of the heterodimer. Genetic data in the worm are consistent with SPT function (sptl-1 RNAi depletes nearly all sphingolipids and is phenocopied by the SPT inhibitor myriocin). This is the core molecular function. Supporting Evidence: file:worm/sptl-1/sptl-1-uniprot.txt The catalytic core is composed of a heterodimer of sptl-1 and sptl-2 or sptl-1 and sptl-3 (By similarity). PMID:21926990 SPTL-1, predicted to condense a fatty acid with serine to form the long-chain-base (LCB) sphinganine as the first committed step in de novo sphingolipid synthesis PMID:38704027 RNAi targeting the first key enzyme (SPT) in the de novo sphingolipid biosynthesis pathway caused a decrease of nearly all sphingolipids in Caenorhabditis elegans. file:worm/sptl-1/sptl-1-bioinformatics/RESULTS.md SPTL-1 is far closer to human SPTLC1 (50.3% identity over the aligned region) than to SPTLC2 (30.1%) |
| GO:0004758 serine C-palmitoyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic assignment from the EC 2.3.1.50 / RHEA:14761 reaction recorded on the UniProt entry. Reason: Same claim as the IBA row; the reaction is the correct SPT reaction and SPTL-1 is an obligate subunit of the heterodimeric enzyme. Caveat recorded in the IBA row (SPTL-1 is the LCB1-type, non-PLP-binding subunit; in C. elegans the physiological acyl-CoA is largely the iso-branched C15 species rather than palmitoyl-CoA). Supporting Evidence: file:worm/sptl-1/sptl-1-uniprot.txt Component of the serine palmitoyltransferase (SPT) that catalyzes the first committed step in sphingolipid biosynthesis, which is the condensation of an acyl-CoA species and L-serine. PMID:23705068 a gene encoding a serine palmitoyltransferase homolog in C. elegans required for d17iso-SPA biosynthesis |
| GO:0005783 endoplasmic reticulum | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT propagation of ER localization from LCB1-clade members with experimental ER data (human SPTLC1, mouse Sptlc1, yeast LCB1, Arabidopsis LCB1, trypanosomatid LCB1s). Reason: Root-organelle synthesis row checked per the organelle policy. The IBD rests on experimental ER localization of SPT in fungi, plants, protists and mammals, a deeply conserved feature of the enzyme; SPTL-1 is inside that clade and retains an N-terminal hydrophobic segment like the single-pass ER membrane anchor of human SPTLC1. No C. elegans localization assay exists, but the organelle claim holds. The ER-membrane sub-compartment is not added as a NEW row because the only independent line is homology (UniProt annotates no transmembrane feature for P91079); the distended ER seen in sptl-1(RNAi) intestine is a phenotype, not a localization. Supporting Evidence: PMID:38704027 SPTL-1 is the C. elegans ortholog of the catalytic subunit of human serine palmitoyltransferase, which is located on the ER (26, 32). |
| GO:0006665 sphingolipid metabolic process | IEA GO_REF:0000041 | MODIFY | Summary: UniPathway mapping (sphingolipid metabolism) to the general metabolic process term. Reason: Correct but general. SPT catalyses the entry step of de novo sphingolipid synthesis, so the supported specific term is sphingolipid biosynthetic process (GO:0030148), an is_a descendant; sptl-1 knockdown depletes nearly all ceramides, glucosylceramides and sphingomyelins in the worm. Proposed replacements: sphingolipid biosynthetic process Supporting Evidence: PMID:38704027 RNAi targeting the first key enzyme (SPT) in the de novo sphingolipid biosynthesis pathway caused a decrease of nearly all sphingolipids in Caenorhabditis elegans. PMID:23705068 sptl-1(−) disrupts all sphingolipid biosynthesis |
| GO:0030170 pyridoxal phosphate binding | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: InterPro2GO from the class-I/II aminotransferase large-domain signature. Reason: SPTL-1 retains the PLP-dependent transferase fold but lacks the Schiff-base lysine that binds PLP (Asn297 aligns with SPTLC2 K379). In the SPT heterodimer the cofactor is bound by the LCB2-type subunit (SPTL-2/SPTL-3 in the worm). The InterPro fold signature over-propagates PLP binding to this non-catalytic subunit, matching the treatment of human SPTLC1. Supporting Evidence: file:worm/sptl-1/sptl-1-bioinformatics/RESULTS.md At the position aligned to the SPTLC2 PLP Schiff-base lysine (K379), SPTL-1 has Asn297, not Lys. |
| GO:0045197 establishment or maintenance of epithelial cell apical/basal polarity | IMP PMID:21926990 Apicobasal domain identities of expanding tubular membranes ... | KEEP AS NON CORE | Summary: sptl-1 RNAi (full text read) converts intestinal apicobasal polarity in larvae, with apical markers (ERM-1, PAR-6, actin) displaced to lateral membranes and ectopic lateral lumens; the phenotype is phenocopied by sptl-2;sptl-3 double RNAi, myriocin and fumonisin B, and is partially rescued by glycosphingolipids. Reason: The IMP is well supported and the curators read the full paper. The paper's model is that glycosphingolipids, the downstream products of the pathway SPTL-1 initiates, are required for polarized apical membrane biogenesis; SPTL-1 itself acts upstream by supplying the long-chain base. Retained as a genuine, experimentally grounded but indirect, non-core process annotation rather than the enzyme's core function. Supporting Evidence: PMID:21926990 Sphingolipid's role in polarity was, however, confirmed via sptl-1(RNAi) phenocopy by: double knockdowns of sptl-2 and sptl-3, two additional C.elegans SPTs (Fig.S6e); feeding Myriocin or Fumonisin B, mycotoxins specifically inhibiting SPT and ceramide synthase (CerS), respectively. PMID:31138658 sptl-1(c363g) homozygous mutants exhibited the same larval lethality and epithelial polarity defect as observed in sptl-1(RNAi) animals |
| GO:0046512 sphingosine biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT propagation of sphingosine biosynthesis from mammalian SPTLC1. Reason: SPT produces 3-ketosphinganine, the precursor of all sphingoid bases. In C. elegans the product is the iso-branched C17 analogue (d17iso-sphinganine/sphingosine), and sptl-1 is required for d17iso-sphingoid base synthesis; loss of sptl-1 lowers the sphingosine that accumulates in sphk-1 mutants. Consistent with the human SPTLC1 treatment. Supporting Evidence: PMID:23705068 a gene encoding a serine palmitoyltransferase homolog in C. elegans required for d17iso-SPA biosynthesis PMID:41191545 Loss of sptl-1 alleviates sphingosine accumulation |
| GO:0046513 ceramide biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT propagation of ceramide biosynthesis from mammalian SPTLC1. Reason: SPT catalyses the first committed step of de novo ceramide synthesis, and in the worm sptl-1 RNAi reduces nearly all ceramide species as measured by LC-MS/MS. The IBD placement covers the LCB1 clade including SPTL-1. Supporting Evidence: PMID:38704027 RNAi targeting the first key enzyme (SPT) in the de novo sphingolipid biosynthesis pathway caused a decrease of nearly all sphingolipids in Caenorhabditis elegans. |
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Download this section (compressed HTML)Q: Does SPTL-1 heterodimerize with both SPTL-2 and SPTL-3 in vivo, and do the two complexes differ in acyl-CoA preference (iso-C15 versus straight-chain palmitoyl-CoA) or tissue distribution?
Q: Is there a C. elegans small subunit (ssSPT/Tsc3-like) or ORMDL ortholog regulating SPTL-1 complexes, and should the worm complex be annotated as GO:0017059 with experimental evidence?
Q: Should the epithelial polarity IMP on SPT subunits be represented in GO-CAM as a downstream requirement for glycosphingolipid products rather than a direct process role of the enzyme?
Experiment: Express SPTL-1 with SPTL-2 or SPTL-3 (in yeast lcb1 lcb2 mutants or insect cells) and assay SPT activity with iso-C15-CoA versus palmitoyl-CoA, with SPTL-1 alone as a control.
Hypothesis: SPTL-1 is required but not sufficient for SPT activity, and the partner subunit sets acyl-CoA preference.
Experiment: Endogenous CRISPR tag of SPTL-1 imaged with ER membrane and Golgi markers in intestine and hypodermis.
Hypothesis: SPTL-1 resides in the ER membrane, as do its orthologs.
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Download this section (compressed HTML)sptl-1 encodes a putative serine palmitoyltransferase required for normal embryonic and larval developement, locomotion, and speed of growth.
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