Fatty acid elongase 3 (Elo3/Sur4/Sre1/Apa1/Vbm1) is a multi-pass endoplasmic reticulum membrane 3-keto-acyl-CoA synthase of the ELO family that catalyses the condensation of an acyl-CoA with malonyl-CoA, the first, rate-limiting reaction of the ER fatty acid elongation cycle. Elo3 forms elongase III, which extends C18-C24 acyl-CoAs and is required for the final C24 to C26 step that produces the C26:0 VLCFA characteristic of yeast ceramide; Ifa38, Phs1 and Tsc13 complete each cycle and Tsc13 co-immunoprecipitates with Elo3. Its active site faces the cytosol and chain length is determined by a lysine near the luminal end of transmembrane helix 6. Elo3 is partially redundant with Elo2 (double mutant inviable). elo3 mutants accumulate C24 VLCFAs, phytosphingosine and inositol phosphorylceramide with little mannosylated sphingolipid, and show pleiotropic membrane phenotypes (plasma membrane H+-ATPase, secretion, endosomal traffic). Isolated as APA1 in a screen for mutants with altered plasma membrane H+-ATPase levels, its deletion impairs glucose regulation of PMA1 expression and reduces expression of the glucose-repressible HXT3 and SNF3 genes, which led to the proposal that it acts in a glucose-signalling pathway; how a fatty acid elongase produces these transcriptional effects is unknown.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005783 endoplasmic reticulum | IDA PMID:12087109 The Saccharomyces cerevisiae YBR159w gene encodes the 3-keto... | ACCEPT | Summary: Han et al. 2002 showed GFP-tagged ELO3 co-localising with the ER elongase components (Ybr159p/Ifa38 co-localises with Elo3p and Tsc13p); ELO3 is an integral ER membrane condensing enzyme. Correct but less specific than ER membrane. Supporting Evidence: PMID:12087109 Green fluorescent protein-tagged Ybr159p co-localizes and co-immunoprecipitates with other elongating enzymes, Elo3p and Tsc13p file:yeast/ELO3/ELO3-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum membrane |
| GO:0005783 endoplasmic reticulum | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA machine-learning rule assigns ER to ELO-family proteins; correct for ELO3, a polytopic ER membrane elongase. Supporting Evidence: file:yeast/ELO3/ELO3-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum membrane |
| GO:0005789 endoplasmic reticulum membrane | EXP PMID:12087109 The Saccharomyces cerevisiae YBR159w gene encodes the 3-keto... | ACCEPT | Summary: UniProt-curated EXP location citing Han et al. 2002 (co-localisation with ER elongase components). ELO3 is a multi-pass ER membrane protein whose active site faces the cytosol. Supporting Evidence: PMID:12087109 Green fluorescent protein-tagged Ybr159p co-localizes and co-immunoprecipitates with other elongating enzymes, Elo3p and Tsc13p file:yeast/ELO3/ELO3-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum membrane PMID:17719544 Mutational analysis revealed that the Elop active site faces the cytosol, whereas VLCFA length is determined by a lysine near the luminal end of an Elop transmembrane helix |
| GO:0005789 endoplasmic reticulum membrane | EXP PMID:14562095 Global analysis of protein localization in budding yeast. | ACCEPT | Summary: Huh et al. 2003 genome-wide GFP survey scored ELO3-GFP at the ER; consistent with all dedicated localisation studies. Supporting Evidence: PMID:14562095 We classify these proteins, representing 75% of the yeast proteome, into 22 distinct subcellular localization categories file:yeast/ELO3/ELO3-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum membrane |
| GO:0005789 endoplasmic reticulum membrane | EXP PMID:9832547 Involvement of long chain fatty acid elongation in the traff... | ACCEPT | Summary: David et al. 1998 (where ELO3 was isolated as VBM1) fractionated HA-tagged protein with resident ER/early Golgi markers, not with secretory vesicles, and described the Vbm proteins as ER-localised membrane proteins. Supporting Evidence: PMID:9832547 Recessive mutations in either VBM1 or VBM2, which encode related ER-localized membrane proteins, allow yeast to grow normally and secrete in the absence of Snc v-SNAREs PMID:9832547 The results from these complimentary strategies suggest a probable ER and, perhaps, early Golgi localization for the Vbm proteins. |
| GO:0005789 endoplasmic reticulum membrane | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA from the ELO/ELOVL family node PTN000125390; all characterised members (yeast Elo1-3, mammalian ELOVL1-7) are ER membrane condensing enzymes, and ELO3 has its own experimental support for this location. Supporting Evidence: file:yeast/ELO3/ELO3-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum membrane PMID:11113186 A similar pattern of staining was observed in cells expressing a chromosomal Elo3p-GFP fusion |
| GO:0005789 endoplasmic reticulum membrane | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location keyword mapping (SL-0097 Endoplasmic reticulum membrane), itself based on the experimental UniProt statement for ELO3. Supporting Evidence: file:yeast/ELO3/ELO3-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum membrane |
| GO:0005829 cytosol | RCA GO_REF:0000123 | REMOVE | Summary: YeastPathways-to-GO-CAM conversion of PWY-5080-1 (very long chain fatty acid biosynthesis I) placed the condensation step 'is_active_in cytosol', apparently a compartment default of the conversion. ELO3 is a multi-pass integral ER membrane protein; only its active site faces the cytosolic side of the membrane. Reason: Computational location default contradicted by direct localisation data; the enzyme is an integral ER membrane protein, not a soluble cytosolic protein, and the ER membrane is already annotated. Supporting Evidence: PMID:17719544 Mutational analysis revealed that the Elop active site faces the cytosol, whereas VLCFA length is determined by a lysine near the luminal end of an Elop transmembrane helix file:yeast/ELO3/ELO3-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum membrane |
| GO:0006633 fatty acid biosynthetic process | IMP PMID:9211877 ELO2 and ELO3, homologues of the Saccharomyces cerevisiae EL... | MODIFY | Summary: Oh et al. 1997 showed elo3 null mutants are defective in VLCFA formation (loss of C26). Correct but generic: the specific process is VLCFA biosynthesis by elongation of pre-existing acyl-CoAs, not de novo synthesis. Proposed replacements: very long-chain fatty acid biosynthetic process Supporting Evidence: PMID:9211877 null mutations of ELO2 and ELO3 produce defects in the formation of very long chain fatty acids PMID:9211877 Elo3p apparently has a broader substrate specificity and is essential for the conversion of 24-carbon acids to 26-carbon species |
| GO:0006892 post-Golgi vesicle-mediated transport | IMP PMID:9832547 Involvement of long chain fatty acid elongation in the traff... | MARK AS OVER ANNOTATED | Summary: David et al. 1998 isolated elo3/vbm1 mutations as suppressors that bypass the Snc v-SNARE requirement for exocytosis. The authors attribute the effect to altered lipid (VLCFA/sphingolipid) synthesis in the ER, not to Elo3 acting in post-Golgi vesicle traffic; Elo3 is not found on secretory vesicles. Reason: Elo3 does none of the work of vesicle transport; trafficking phenotypes are downstream consequences of membrane lipid composition. Retained as over-annotation rather than removed because it is an IMP phenotype from the cited study. Supporting Evidence: PMID:9832547 Recessive mutations in either VBM1 or VBM2, which encode related ER-localized membrane proteins, allow yeast to grow normally and secrete in the absence of Snc v-SNAREs PMID:9832547 act at the level of lipid synthesis to affect the ability of secretory vesicles to sort and deliver protein cargo PMID:9832547 The results from these complimentary strategies suggest a probable ER and, perhaps, early Golgi localization for the Vbm proteins. |
| GO:0009922 fatty acid elongase activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA from ELO/ELOVL family node PTN000125390. 3-keto-acyl-CoA synthase (condensing) activity is the defining activity of the family and ELO3 has direct biochemical support (elongase activity lost in the mutant; reconstitution with purified components). Supporting Evidence: PMID:12684876 Elongases I, II and III are specifically inactivated in, respectively, elo1, elo2 and elo3 mutants PMID:17719544 Proteoliposomes reconstituted here from purified membrane components-an elongase protein (Elop), a novel dehydratase, and two reductases-catalyzed repeated rounds of two-carbon addition |
| GO:0009922 fatty acid elongase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Combined IEA (InterPro IPR002076 ELO family, RHEA:32727, EC 2.3.1.199) for the VLC 3-oxoacyl-CoA synthase reaction; matches the UniProt-curated catalytic activity of ELO3. Supporting Evidence: file:yeast/ELO3/ELO3-uniprot.txt Reaction=a very-long-chain acyl-CoA + malonyl-CoA + H(+) = a very-long- |
| GO:0009922 fatty acid elongase activity | IMP PMID:12684876 Functional differentiation and selective inactivation of mul... | ACCEPT | Summary: Rossler et al. 2003 defined three microsomal elongase activities by primer specificity in vitro and showed elongase III is specifically lost in the elo3 mutant. Elo3 (elongase III) elongates C18-C24 acyl-CoAs and is required for the final C24 to C26 step. Supporting Evidence: PMID:12684876 Elongases I, II and III are specifically inactivated in, respectively, elo1, elo2 and elo3 mutants PMID:12684876 Elongase II elongates palmitoyl-CoA and stearoyl-CoA up to C22 fatty acids, and elongase III synthesizes 20-26-carbon fatty acids from C18-CoA primers |
| GO:0009922 fatty acid elongase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways PWY-5080-1 assigns the condensation step (long-chain acyl-CoA + malonyl-CoA -> 3-oxoacyl-CoA + CO2 + CoA) to ELO3; this assignment is correct and matches the experimental data. Supporting Evidence: PMID:12684876 Elongases I, II and III are specifically inactivated in, respectively, elo1, elo2 and elo3 mutants file:yeast/ELO3/ELO3-uniprot.txt Reaction=a very-long-chain acyl-CoA + malonyl-CoA + H(+) = a very-long- |
| GO:0016020 membrane | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping from IPR002076 (ELO family) to 'membrane'; correct but uninformative given the experimentally established ER membrane location. Proposed replacements: endoplasmic reticulum membrane Supporting Evidence: file:yeast/ELO3/ELO3-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum membrane |
| GO:0019367 fatty acid elongation, saturated fatty acid | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA (PTN000125390) for elongation of saturated fatty acids. Yeast VLCFAs (C20-C26, sphingolipid C26:0) are saturated, and ELO3 elongates saturated C16:0/C18:0 primers, so this term is appropriate. Supporting Evidence: PMID:12684876 Elongase II elongates palmitoyl-CoA and stearoyl-CoA up to C22 fatty acids, and elongase III synthesizes 20-26-carbon fatty acids from C18-CoA primers PMID:9211877 produce the 26-carbon very long chain fatty acids that are precursors for ceramide and sphingolipids |
| GO:0030148 sphingolipid biosynthetic process | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: PAINT IBA for sphingolipid biosynthesis. ELO3 supplies the VLCFA acyl-CoA that ceramide synthase amide-links to the long-chain base; it does not catalyse a sphingolipid-forming step itself. Supporting Evidence: PMID:9211877 produce the 26-carbon very long chain fatty acids that are precursors for ceramide and sphingolipids PMID:9211877 Disruption of either gene reduces cellular sphingolipid levels and results in the accumulation of the long chain base, phytosphingosine |
| GO:0030148 sphingolipid biosynthetic process | IMP PMID:9211877 ELO2 and ELO3, homologues of the Saccharomyces cerevisiae EL... | KEEP AS NON CORE | Summary: Oh et al. 1997: disruption of ELO3 reduces sphingolipid levels and causes phytosphingosine accumulation. Consistent with an upstream precursor-supply role. Supporting Evidence: PMID:9211877 Disruption of either gene reduces cellular sphingolipid levels and results in the accumulation of the long chain base, phytosphingosine PMID:9211877 produce the 26-carbon very long chain fatty acids that are precursors for ceramide and sphingolipids |
| GO:0030497 fatty acid elongation | IMP PMID:9211877 ELO2 and ELO3, homologues of the Saccharomyces cerevisiae EL... | TOO GENERAL | Summary: Oh et al. 1997: ELO3 null mutants are defective in VLCFA formation; ELO3 encodes a component of the membrane-bound fatty acid elongation system. Correct process; VLCFA biosynthesis is the more specific term. Supporting Evidence: PMID:9211877 null mutations of ELO2 and ELO3 produce defects in the formation of very long chain fatty acids PMID:9211877 Elo3p apparently has a broader substrate specificity and is essential for the conversion of 24-carbon acids to 26-carbon species |
| GO:0032511 late endosome to vacuole transport via multivesicular body sorting pathway | IGI PMID:23325927 Effects on vesicular transport pathways at the late endosome... | MARK AS OVER ANNOTATED | Summary: Obara et al. 2013: sur4 deletion is synthetically sick with vps21 (Rab5) and impairs endosomal trafficking (CPY, endocytosis) in the double mutant. This reflects a requirement of the endosomal membrane for VLCFAs rather than a transport function of the elongase. Reason: Genetic-interaction phenotype downstream of lipid composition; the ER-resident elongase does not participate in late endosome to vacuole transport. Kept as over-annotation (IGI) rather than removed. Supporting Evidence: PMID:23325927 These results suggest that, of all the intracellular trafficking pathways, requirement of VLCFAs is especially high in the endosomal pathways. |
| GO:0034625 fatty acid elongation, monounsaturated fatty acid | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: PAINT IBA (PTN000125390) for monounsaturated fatty acid elongation, propagated from mammalian ELOVLs (e.g. ELOVL1/3/7). Yeast VLCFAs used in sphingolipids are saturated and no experiment shows ELO3 elongating C16:1/C18:1 in vivo. Reason: Plausible as a minor in vitro capability of the condensing enzyme but not shown for yeast; the physiological substrates are saturated acyl-CoAs. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN000125390 SUPPORTS SOURCE BUT NOT TARGET Node spans all ELO/ELOVL condensing enzymes; MUFA elongation is documented for vertebrate/insect/amoebozoan members but no yeast Elo has been shown to elongate monounsaturated acyl-CoAs in vivo. Supporting Evidence: PMID:12684876 Elongase II elongates palmitoyl-CoA and stearoyl-CoA up to C22 fatty acids, and elongase III synthesizes 20-26-carbon fatty acids from C18-CoA primers PMID:9211877 produce the 26-carbon very long chain fatty acids that are precursors for ceramide and sphingolipids |
| GO:0034626 fatty acid elongation, polyunsaturated fatty acid | IBA GO_REF:0000033 | REMOVE | Summary: PAINT IBA (PTN000125390) for polyunsaturated fatty acid elongation, propagated from PUFA-elongating ELOVL2/4/5 orthologues. S. cerevisiae makes no polyunsaturated fatty acids (it has only the Ole1 delta-9 desaturase), so there is no PUFA substrate for ELO3 in vivo. Reason: Biologically inapplicable in this organism: no PUFA synthesis in S. cerevisiae; the IBA node spans PUFA-specific ELOVL subfamilies whose specificity is not inherited by the yeast saturated-VLCFA elongases. Propagation Review Root cause: PROPAGATION BAD Failure modes: LINEAGE OR TAXON MISMATCH Sources checked: PANTHER:PTN000125390 SUPPORTS SOURCE BUT NOT TARGET PUFA elongation is grounded in animal ELOVL PUFA elongases; S. cerevisiae synthesises no polyunsaturated fatty acids, so the process does not occur in the target lineage. Supporting Evidence: PMID:12684876 Elongase II elongates palmitoyl-CoA and stearoyl-CoA up to C22 fatty acids, and elongase III synthesizes 20-26-carbon fatty acids from C18-CoA primers PMID:9211877 produce the 26-carbon very long chain fatty acids that are precursors for ceramide and sphingolipids |
| GO:0042761 very long-chain fatty acid biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA (PTN000125390) for VLCFA biosynthesis; the core process of the ELO family and directly supported for ELO3 by mutant fatty-acid profiles and in vitro elongation. Supporting Evidence: PMID:9211877 null mutations of ELO2 and ELO3 produce defects in the formation of very long chain fatty acids PMID:12684876 Elongase II elongates palmitoyl-CoA and stearoyl-CoA up to C22 fatty acids, and elongase III synthesizes 20-26-carbon fatty acids from C18-CoA primers |
| GO:0042761 very long-chain fatty acid biosynthetic process | IMP PMID:23325927 Effects on vesicular transport pathways at the late endosome... | ACCEPT | Summary: Obara et al. 2013 assayed microsomal FA elongation: sur4 deletion membranes were impaired in elongation beyond C22-CoA. Direct IMP support for the core process. Supporting Evidence: PMID:23325927 However, elongations beyond C18-CoA and C22-CoA were largely impaired in fen1 Ξ and sur4 Ξ cells, respectively. |
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Download this section (compressed HTML)Q: Is the C24 to C26 step strictly Elo3-specific in vivo, or can elevated Elo2 levels partially supply C26 VLCFA?
Q: Which elo3/sur4 phenotypes (Pma1 activity, endosomal traffic) are caused by loss of C26 sphingolipids per se rather than accumulation of long-chain bases?
Experiment: Measure C24-CoA condensation in microsomes from elo3 and elo2 elo3 (rescued by a regulatable ELO3 allele) strains, and in proteoliposomes containing purified Elo2 versus Elo3.
Hypothesis: Elo3 is the sole yeast enzyme able to condense C24-CoA.
Elongase; involved in fatty acid and sphingolipid biosynthesis; synthesizes very long chain 20-26-carbon fatty acids from C18-CoA primers; involved in regulation of sphingolipid biosynthesis; lethality of the elo2 elo3 double null mutation is functionally complemented by human ELOVL1 and weakly complemented by human ELOVL3 or ELOV7
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