Zebrafish fads2 encodes a front-end fatty acid desaturase of the endoplasmic reticulum membrane, carrying an N-terminal cytochrome b5 domain and the three catalytic histidine boxes typical of the family (PMID:11724940). Unusually for a vertebrate, the single enzyme is bifunctional: expressed in yeast it converts linoleate and alpha-linolenate to their delta-6 products and also converts 20:3n-6 and 20:4n-3 to arachidonate and eicosapentaenoate, i.e. it performs both the delta-6 and the delta-5 desaturation of the long-chain polyunsaturated fatty acid pathway (PMID:11724940). It uses molecular oxygen and electrons delivered through cytochrome b5, and in vivo it also acts with delta-8 specificity on elongated C20 substrates, giving an alternative route to LC-PUFA (PMID:35456508). Because zebrafish rely on this one enzyme for the first, rate-limiting steps, partial loss of function lowers omega-3 and omega-6 LC-PUFA in eggs and impairs female reproduction (PMID:35456508); morpholino knockdown also reduces liver size in embryos (PMID:23813869).
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0016020 membrane | IBA GO_REF:0000033 | MODIFY | Summary: IBA from the front-end desaturase node (PTN002321280) for the generic parent term membrane. Zebrafish Fads2 is a polytopic ER-membrane protein with an N-terminal cytochrome b5 domain (PMID:11724940), and UniProt places it in the ER membrane. Reason: The node correctly infers membrane residence for the family, but the informative child is already supported for this protein: UniProt assigns the ER membrane and the enzyme uses the ER electron-transfer chain. Replace the parent with GO:0005789, which the gene already carries by IEA. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN002321280 SUPPORTS TRANSFER Front-end desaturase node; membrane residence is correctly inherited, but the node spans bacterial, plant and animal members whose membranes differ, so it can only assert the generic parent. UniProtKB:O60427 Β· Human FADS1 SUPPORTS TRANSFER Vertebrate donor of the same family; the vertebrate members are ER-membrane enzymes, the level at which the location should be recorded. Proposed replacements: endoplasmic reticulum membrane Supporting Evidence: file:DANRE/fads2/fads2-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum membrane PMID:11724940 The 1,590-bp sequence specifies a protein that, in common with other fatty acid desaturases, contains an N-terminal cytochrome b(5) domain and three histidine boxes, believed to be involved in catalysis. |
| GO:0005789 endoplasmic reticulum membrane | IEA GO_REF:0000044 | ACCEPT | Summary: IEA from the UniProt subcellular-location vocabulary (SL-0097). Front-end desaturases are ER-membrane enzymes that draw electrons from NADH-cytochrome b5 reductase and cytochrome b5; zebrafish Fads2 carries its own N-terminal cytochrome b5 domain (PMID:11724940). Deep research adds zebrafish-specific co-localization of Fads2 with the ER marker ERp57, which UniProt does not record. Reason: The ER membrane is where the desaturation happens, and the assignment follows the curated UniProt location for this entry rather than a bare prediction. Accepted as the location of the core activity. No zebrafish imaging experiment is cited by UniProt, so this is by similarity. Supporting Evidence: file:DANRE/fads2/fads2-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum membrane PMID:11724940 The 1,590-bp sequence specifies a protein that, in common with other fatty acid desaturases, contains an N-terminal cytochrome b(5) domain and three histidine boxes, believed to be involved in catalysis. file:DANRE/fads2/fads2-deep-research-falcon.md Co-localization with an ER marker (ERp57) supports ER association. |
| GO:0006629 lipid metabolic process | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping of IPR005804 (fatty acid desaturase domain) to the broad parent lipid metabolic process. The specific pathway is known for this enzyme. Reason: Not wrong but uninformative: the zebrafish enzyme desaturates C18 and C20 polyunsaturated acyl chains (PMID:11724940), which UniProt records as the polyunsaturated fatty acid biosynthesis pathway. Replace with GO:0006636, which the gene already carries by UniPathway IEA. Proposed replacements: unsaturated fatty acid biosynthetic process Supporting Evidence: file:DANRE/fads2/fads2-uniprot.txt PATHWAY: Lipid metabolism; polyunsaturated fatty acid biosynthesis. PMID:11724940 The zebrafish Delta5/Delta6 desaturase may represent a component of a prototypic vertebrate polyunsaturated fatty acids biosynthesis pathway. |
| GO:0016213 acyl-CoA 6-desaturase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Rhea/EC-based IEA (RHEA:47140, RHEA:47144, EC 1.14.19.3) for acyl-CoA 6-desaturase activity. This is the activity UniProt records from the zebrafish experiment: expression of the cDNA in yeast conferred conversion of linoleate and alpha-linolenate to their delta-6 products (PMID:11724940). Reason: Directly demonstrated for this protein by heterologous expression, and the delta-6 step is the rate-limiting entry into LC-PUFA synthesis. CRISPR crispants confirm the same step is impaired in vivo (PMID:35456508). Core molecular function. Supporting Evidence: PMID:11724940 When the zebrafish cDNA was expressed in Saccharomyces cerevisiae it conferred the ability to convert linoleic acid (18:2n-6) and alpha-linolenic acid (18:3n-3) to their corresponding Delta6 desaturated products, 18:3n-6 and 18:4n-3. PMID:35456508 Our data suggest an impaired pathway of the LC-PUFA biosynthesis of the Ο6 and Ο3 series in the first-rate limiting steps of the conversion of linoleic acid (LA) into Ξ³-linolenic acid (GLA), and Ξ±-linolenic acid (ALA) into stearidonic acid (SDA), respectively, finally resulting in bad-quality eggs. file:DANRE/fads2/fads2-uniprot.txt Fatty acid desaturase with bifunctional delta-5 and delta-6 |
| GO:0016491 oxidoreductase activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping of IPR012171 to the top-level term oxidoreductase activity. Reason: The parent of every redox enzyme adds nothing here: the substrate and regiospecificity are known from direct assay (PMID:11724940) and are captured by the acyl-CoA desaturase terms the gene already carries. Replace with those two. Proposed replacements: acyl-CoA 6-desaturase activity acyl-CoA (8-3)-desaturase activity Supporting Evidence: PMID:11724940 it conferred on the yeast the ability to convert di-homo-gamma-linoleic acid (20:3n-6) and eicosatetraenoic acid (20:4n-3) to arachidonic acid (20:4n-6) and eicosapentaenoic acid (20:5n-3), respectively, indicating that the zebrafish gene encodes an enzyme having both Delta5 and Delta6 desaturase activity. file:DANRE/fads2/fads2-uniprot.txt Fatty acid desaturase with bifunctional delta-5 and delta-6 |
| GO:0062076 acyl-CoA (8-3)-desaturase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Rhea/EC-based IEA (RHEA:46420, RHEA:46424, EC 1.14.19.44) for acyl-CoA (8-3)-desaturase activity, i.e. insertion of a double bond three carbons from the existing delta-8 unsaturation - the delta-5 activity of the bifunctional enzyme. Yeast expression converted 20:3n-6 and 20:4n-3 to arachidonate and EPA (PMID:11724940). Reason: Directly demonstrated for the zebrafish protein in the same experiment that showed the delta-6 activity, which is what makes this desaturase bifunctional and unusual among vertebrates (PMID:11724940). Core molecular function alongside GO:0016213. Supporting Evidence: PMID:11724940 it conferred on the yeast the ability to convert di-homo-gamma-linoleic acid (20:3n-6) and eicosatetraenoic acid (20:4n-3) to arachidonic acid (20:4n-6) and eicosapentaenoic acid (20:5n-3), respectively, indicating that the zebrafish gene encodes an enzyme having both Delta5 and Delta6 desaturase activity. file:DANRE/fads2/fads2-uniprot.txt Fatty acid desaturase with bifunctional delta-5 and delta-6 |
| GO:0006636 unsaturated fatty acid biosynthetic process | IEA GO_REF:0000041 | ACCEPT | Summary: IEA from UniPathway UPA00658 for unsaturated fatty acid biosynthesis. Zebrafish Fads2 performs the first, rate-limiting desaturation of dietary C18 precursors and the delta-5 step toward arachidonate and EPA (PMID:11724940); CRISPR crispants show both first steps impaired in vivo, with an alternative delta-8 route used as a bypass (PMID:35456508). Reason: The enzyme performs steps of this pathway itself, so participation is direct rather than inferred from a phenotype. This is the process the core activities carry out. Supporting Evidence: PMID:11724940 The zebrafish Delta5/Delta6 desaturase may represent a component of a prototypic vertebrate polyunsaturated fatty acids biosynthesis pathway. PMID:35456508 Our data suggest an impaired pathway of the LC-PUFA biosynthesis of the Ο6 and Ο3 series in the first-rate limiting steps of the conversion of linoleic acid (LA) into Ξ³-linolenic acid (GLA), and Ξ±-linolenic acid (ALA) into stearidonic acid (SDA), respectively, finally resulting in bad-quality eggs. file:DANRE/fads2/fads2-uniprot.txt PATHWAY: Lipid metabolism; polyunsaturated fatty acid biosynthesis. |
| GO:0001889 liver development | IMP PMID:23813869 Functional validation of GWAS gene candidates for abnormal l... | KEEP AS NON CORE | Summary: ZFIN IMP from a morpholino screen of human GWAS liver-trait candidates (PMID:23813869): fads2 knockdown reduced fabp10a expression and increased the proportion of embryos with small livers at 72 hpf, a statistically significant effect among 8 of 14 genes tested. Reason: The observation is real and specific to fads2 among the screened genes, but a desaturase does no work in hepatic specification or growth: the phenotype follows from depleting LC-PUFA that the liver needs. Morpholino-only evidence in a multi-gene screen. Kept as non-core rather than removed. Supporting Evidence: PMID:23813869 knockdown of cpn1, trib1, fads2, slc2a2 or samm50 all resulted in diminished fabp10a expression and a greater proportion of smaller livers compared with controls (Fig. PMID:23813869 Knockdown of 8/14 genes (pnpla3, trib1, slc2a2, mapk10, cpn1, fads2, pklr and samm50) by ATG-site morpholino injection decreased the proportion of embryos with a small liver size in a statistically significant manner |
| GO:0006629 lipid metabolic process | IBA GO_REF:0000033 | MODIFY | Summary: IBA for the same broad parent from the desaturase node (PTN002321280), whose donors include plant, nematode, Dictyostelium, mycobacterial and mammalian desaturases. At that phylogenetic depth only "acts on lipids" is safe to assert. Reason: Same term and same argument as the InterPro IEA row, so the same action: the zebrafish enzyme has a known, specific pathway role (PMID:11724940, UniProt PATHWAY), and GO:0006636 unsaturated fatty acid biosynthetic process states it. The node placement itself is sound; it is the granularity that is wrong for a gene this well characterized. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN002321280 SUPPORTS TRANSFER Deep desaturase node spanning plants, fungi, nematodes and vertebrates; lipid metabolism is the only process term valid across all of them, so the generic parent is a consequence of node depth, not an error. UniProtKB:O60427 Β· Human FADS1 SUPPORTS TRANSFER Vertebrate front-end desaturase donor; in vertebrates the process is specifically PUFA biosynthesis. Proposed replacements: unsaturated fatty acid biosynthetic process Supporting Evidence: file:DANRE/fads2/fads2-uniprot.txt PATHWAY: Lipid metabolism; polyunsaturated fatty acid biosynthesis. PMID:11724940 When the zebrafish cDNA was expressed in Saccharomyces cerevisiae it conferred the ability to convert linoleic acid (18:2n-6) and alpha-linolenic acid (18:3n-3) to their corresponding Delta6 desaturated products, 18:3n-6 and 18:4n-3. |
| GO:0016717 oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water | IBA GO_REF:0000033 | MODIFY | Summary: IBA from the desaturase node (PTN002321280) for the reaction-class term: two donors oxidized, O2 reduced to two waters. Verified via QuickGO, this is the generic front-end desaturase chemistry, correct for Fads2 but silent about chain length and double-bond position. Reason: The node placement is right - this chemistry is what the whole desaturase family does - but for zebrafish fads2 the positional specificity was measured directly in yeast (delta-6 on C18, delta-5 on C20; PMID:11724940), so the substrate-specific children should carry the molecular function. Same replacement as the GO:0016491 IEA row, keeping the actions consistent across the generic MF terms. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN002321280 SUPPORTS TRANSFER Front-end desaturase node; the redox chemistry is genuinely ancestral and inherited, but regiospecificity varies among descendants so the node cannot assert it. UniProtKB:O60427 Β· Human FADS1 SUPPORTS TRANSFER Characterized vertebrate donor; in vertebrates the family members are assigned specific acyl-CoA desaturase activities rather than the reaction class. Proposed replacements: acyl-CoA 6-desaturase activity acyl-CoA (8-3)-desaturase activity Supporting Evidence: PMID:11724940 When the zebrafish cDNA was expressed in Saccharomyces cerevisiae it conferred the ability to convert linoleic acid (18:2n-6) and alpha-linolenic acid (18:3n-3) to their corresponding Delta6 desaturated products, 18:3n-6 and 18:4n-3. PMID:11724940 it conferred on the yeast the ability to convert di-homo-gamma-linoleic acid (20:3n-6) and eicosatetraenoic acid (20:4n-3) to arachidonic acid (20:4n-6) and eicosapentaenoic acid (20:5n-3), respectively, indicating that the zebrafish gene encodes an enzyme having both Delta5 and Delta6 desaturase activity. |
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Download this section (compressed HTML)Q: Does zebrafish Fads2 also carry out the C24 delta-6 desaturation of the Sprecher pathway needed for DHA synthesis, or is that step performed by another enzyme?
Q: Is the delta-8 activity inferred from crispant flux (PMID:35456508) a genuine property of the purified enzyme, and how does its rate compare with the delta-6 and delta-5 activities?
Experiment: Express the zebrafish cDNA in yeast as in PMID:11724940 but supply eicosadienoic (20:2n-6) and eicosatrienoic (20:3n-3) acids, and quantify delta-8 products by GC-MS alongside the delta-6 and delta-5 substrates to measure all three activities in one system.
Hypothesis: Zebrafish Fads2 is a trifunctional delta-6/delta-5/delta-8 desaturase.
Type: heterologous expression and GC-MS
Experiment: Repeat the knockdown in a stable fads2 mutant line and test rescue by dietary or injected arachidonate/EPA, scoring fabp10a expression and liver size at 72 hpf as in PMID:23813869.
Hypothesis: The small-liver phenotype of fads2 morphants reflects LC-PUFA depletion rather than a hepatic function of the protein.
Type: genetic rescue
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