IFA38 (YBR159W) encodes the very-long-chain 3-oxoacyl-CoA reductase (3-ketoacyl-CoA reductase, KAR) of the endoplasmic reticulum fatty acid elongation system, an SDR-family enzyme orthologous to mammalian HSD17B12. It catalyses the NADPH-dependent reduction of 3-oxoacyl-CoA intermediates formed by the Elo2/Elo3 condensing enzymes to (3R)-3-hydroxyacyl-CoA, the second of the four reactions that add two carbons per cycle to make the C20-C26 very long-chain fatty acids used for ceramide and sphingolipid synthesis. Ifa38 resides in the ER membrane, co-localises and co-immunoprecipitates with Elo3 and Tsc13, and is shared by elongases II and III. ifa38 null cells are viable but grow very slowly, have reduced VLCFA, accumulate long-chain bases, medium-chain ceramides and 3-hydroxy fatty acids, and also show reduced 3-hydroxyacyl-CoA dehydration, suggesting Ifa38 supports Phs1 activity; residual reductase activity depends on Ayr1, and the ifa38 ayr1 double mutant is inviable. Ifa38 also interacts physically with the translation initiation factor eIF2B.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005783 endoplasmic reticulum | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA from the very-long-chain 3-oxoacyl-CoA reductase (KAR/HSD17B12) node PTN002454146; ER residence is shared by all characterised members and Ifa38 has its own experimental support. Supporting Evidence: file:yeast/IFA38/IFA38-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum membrane PMID:12087109 Green fluorescent protein-tagged Ybr159p co-localizes and co-immunoprecipitates with other elongating enzymes, Elo3p and Tsc13p |
| GO:0005783 endoplasmic reticulum | IDA PMID:12087109 The Saccharomyces cerevisiae YBR159w gene encodes the 3-keto... | ACCEPT | Summary: Han et al. 2002 showed GFP-Ybr159p/Ifa38 co-localising with the ER elongase enzymes Elo3 and Tsc13. Correct, though ER membrane is more precise. Supporting Evidence: PMID:12087109 Green fluorescent protein-tagged Ybr159p co-localizes and co-immunoprecipitates with other elongating enzymes, Elo3p and Tsc13p |
| GO:0005783 endoplasmic reticulum | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from IPR027533 (very-long-chain 3-oxoacyl-CoA reductase, fungi) to ER; correct for Ifa38. Supporting Evidence: file:yeast/IFA38/IFA38-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum membrane |
| GO:0005789 endoplasmic reticulum membrane | IDA PMID:23263984 The yeast eukaryotic translation initiation factor 2B transl... | ACCEPT | Summary: Browne et al. 2013 showed Ybr159w/Ifa38 localises to the ER membrane (fractionation/microscopy) while studying its interaction with eIF2B. Supporting Evidence: PMID:23263984 Although YBR159W localizes to the endoplasmic reticulum membrane file:yeast/IFA38/IFA38-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum membrane |
| GO:0005789 endoplasmic reticulum membrane | IEA GO_REF:0000120 | ACCEPT | Summary: UniProt subcellular-location / UniRule (HAMAP MF_03107) mapping to ER membrane; consistent with experimental localisation. Supporting Evidence: file:yeast/IFA38/IFA38-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum membrane PMID:23263984 Although YBR159W localizes to the endoplasmic reticulum membrane |
| GO:0005829 cytosol | RCA GO_REF:0000123 | REMOVE | Summary: YeastPathways PWY-5080-1 GO-CAM conversion placed the 3-ketoreductase step 'is_active_in cytosol', a compartment default. Ifa38 is an ER membrane-anchored SDR enzyme; the elongation cycle is ER-bound. Reason: Computational location default contradicted by experimental ER membrane localisation; ER membrane is already annotated. Supporting Evidence: PMID:23263984 Although YBR159W localizes to the endoplasmic reticulum membrane file:yeast/IFA38/IFA38-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum membrane |
| GO:0006633 fatty acid biosynthetic process | IEA GO_REF:0000041 | MODIFY | Summary: UniPathway UPA00094 (fatty acid biosynthesis) mapping. Correct in a broad sense but Ifa38 acts in microsomal elongation of pre-existing acyl-CoAs to VLCFAs, not in de novo FAS-dependent synthesis. Proposed replacements: very long-chain fatty acid biosynthetic process Supporting Evidence: PMID:12087109 The YBR159w gene encodes the major 3-ketoreductase activity of the elongase system of enzymes required for very long-chain fatty acid (VLCFA) synthesis |
| GO:0018454 acetoacetyl-CoA reductase activity | IEA GO_REF:0000116 | MODIFY | Summary: IEA from Rhea reactions (VLC 3-oxoacyl-CoA reductions, e.g. RHEA:39151/39171) mapped to 'acetoacetyl-CoA reductase activity' (EC 1.1.1.36). The reaction chemistry (NADPH reduction to (R)-3-hydroxyacyl-CoA) is right, but the GO term is named for the C4 PHB-pathway enzyme and is not an ancestor of the VLC-specific term that describes Ifa38. Proposed replacements: very-long-chain 3-oxoacyl-CoA reductase activity Supporting Evidence: file:yeast/IFA38/IFA38-uniprot.txt Reaction=a very-long-chain (3R)-3-hydroxyacyl-CoA + NADP(+) = a very- PMID:12087109 In vitro elongation assays confirm that the ybr159Delta mutant is deficient in the reduction of the 3-ketoacyl intermediates of fatty acid elongation |
| GO:0018454 acetoacetyl-CoA reductase activity | RCA GO_REF:0000123 | MODIFY | Summary: YeastPathways PWY-5080-1 assigns the 3-oxoacyl-CoA reduction (EC 1.1.1.36 in YeastCyc) to Ifa38. Step assignment correct; the GO term chosen by the EC mapping (acetoacetyl-CoA reductase) is the wrong chain-length class. Proposed replacements: very-long-chain 3-oxoacyl-CoA reductase activity Supporting Evidence: PMID:12087109 The YBR159w gene encodes the major 3-ketoreductase activity of the elongase system of enzymes required for very long-chain fatty acid (VLCFA) synthesis file:yeast/IFA38/IFA38-uniprot.txt Reaction=a very-long-chain (3R)-3-hydroxyacyl-CoA + NADP(+) = a very- |
| GO:0030148 sphingolipid biosynthetic process | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: ARBA rule for sphingolipid biosynthesis. Ifa38 supplies VLCFA-CoA used by ceramide synthase; ifa38 mutants accumulate long-chain bases and medium-chain ceramides. Upstream precursor role, not a sphingolipid biosynthetic step. Supporting Evidence: PMID:12087109 These phenotypes include reduced VLCFA synthesis, accumulation of high levels of dihydrosphingosine and phytosphingosine, and accumulation of medium-chain ceramides |
| GO:0030148 sphingolipid biosynthetic process | IMP PMID:23263984 The yeast eukaryotic translation initiation factor 2B transl... | KEEP AS NON CORE | Summary: Browne et al. 2013 (IMP); VLCFA-pathway mutants affect sphingolipid synthesis. Consistent with Ifa38's precursor-supply role; kept as non-core. Supporting Evidence: PMID:23263984 very-long-chain fatty acid (VLCFA) synthesis keto-reductase enzyme YBR159W PMID:12087109 These phenotypes include reduced VLCFA synthesis, accumulation of high levels of dihydrosphingosine and phytosphingosine, and accumulation of medium-chain ceramides |
| GO:0030497 fatty acid elongation | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA (PTN002454146): 3-ketoacyl-CoA reduction is the second step of every elongation cycle; experimentally supported for Ifa38. Supporting Evidence: PMID:12087109 In vitro elongation assays confirm that the ybr159Delta mutant is deficient in the reduction of the 3-ketoacyl intermediates of fatty acid elongation PMID:12684876 Elongases II and III share the same 3-ketoacyl reductase, which is encoded by the YBR159w gene |
| GO:0030497 fatty acid elongation | IEA GO_REF:0000120 | ACCEPT | Summary: InterPro/UniRule (IPR027533, MF_03107) mapping to fatty acid elongation; correct. Supporting Evidence: PMID:12087109 The YBR159w gene encodes the major 3-ketoreductase activity of the elongase system of enzymes required for very long-chain fatty acid (VLCFA) synthesis |
| GO:0030497 fatty acid elongation | IMP PMID:12087109 The Saccharomyces cerevisiae YBR159w gene encodes the 3-keto... | ACCEPT | Summary: Han et al. 2002: ybr159 mutant microsomes are deficient in reducing 3-ketoacyl intermediates and the mutant has reduced VLCFA synthesis. Supporting Evidence: PMID:12087109 In vitro elongation assays confirm that the ybr159Delta mutant is deficient in the reduction of the 3-ketoacyl intermediates of fatty acid elongation PMID:12087109 These phenotypes include reduced VLCFA synthesis, accumulation of high levels of dihydrosphingosine and phytosphingosine, and accumulation of medium-chain ceramides |
| GO:0042761 very long-chain fatty acid biosynthetic process | IMP PMID:23263984 The yeast eukaryotic translation initiation factor 2B transl... | ACCEPT | Summary: Browne et al. 2013 analysed the ybr159w null and other VLCFA-pathway mutants; curated IMP for VLCFA biosynthesis is consistent with Han et al. 2002 and Rossler et al. 2003. Supporting Evidence: PMID:23263984 very-long-chain fatty acid (VLCFA) synthesis keto-reductase enzyme YBR159W PMID:12087109 The YBR159w gene encodes the major 3-ketoreductase activity of the elongase system of enzymes required for very long-chain fatty acid (VLCFA) synthesis |
| GO:0042761 very long-chain fatty acid biosynthetic process | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways PWY-5080-1 assignment of the 3-ketoreductase step to Ifa38; correct. Supporting Evidence: PMID:12087109 The YBR159w gene encodes the major 3-ketoreductase activity of the elongase system of enzymes required for very long-chain fatty acid (VLCFA) synthesis PMID:12684876 Elongases II and III share the same 3-ketoacyl reductase, which is encoded by the YBR159w gene |
| GO:0045703 ketoreductase activity | IEA GO_REF:0000120 | MODIFY | Summary: InterPro/UniRule mapping to generic 'ketoreductase activity'; true but uninformative. The specific activity is VLC 3-oxoacyl-CoA reduction. Proposed replacements: very-long-chain 3-oxoacyl-CoA reductase activity Supporting Evidence: file:yeast/IFA38/IFA38-uniprot.txt Reaction=a very-long-chain (3R)-3-hydroxyacyl-CoA + NADP(+) = a very- |
| GO:0045703 ketoreductase activity | IMP PMID:12087109 The Saccharomyces cerevisiae YBR159w gene encodes the 3-keto... | MODIFY | Summary: Han et al. 2002: ybr159 mutant microsomes fail to reduce 3-ketoacyl-CoA elongation intermediates. The generic ketoreductase term should be replaced by the VLC 3-oxoacyl-CoA reductase term. Proposed replacements: very-long-chain 3-oxoacyl-CoA reductase activity Supporting Evidence: PMID:12087109 In vitro elongation assays confirm that the ybr159Delta mutant is deficient in the reduction of the 3-ketoacyl intermediates of fatty acid elongation PMID:12684876 Inactivation of YBR159w inhibits in vitro fatty acid elongation after the first condensation reaction |
| GO:0141040 very-long-chain 3-oxoacyl-CoA reductase activity | EXP PMID:12087109 The Saccharomyces cerevisiae YBR159w gene encodes the 3-keto... | ACCEPT | Summary: Han et al. 2002 identified Ybr159w as the major 3-ketoreductase of the microsomal elongase; Rossler et al. 2003 showed elongases II and III share this reductase. Core activity. Supporting Evidence: PMID:12087109 The YBR159w gene encodes the major 3-ketoreductase activity of the elongase system of enzymes required for very long-chain fatty acid (VLCFA) synthesis PMID:12087109 In vitro elongation assays confirm that the ybr159Delta mutant is deficient in the reduction of the 3-ketoacyl intermediates of fatty acid elongation PMID:12684876 Elongases II and III share the same 3-ketoacyl reductase, which is encoded by the YBR159w gene |
| GO:0141040 very-long-chain 3-oxoacyl-CoA reductase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Combined IEA (RHEA:48680, EC 1.1.1.330) for VLC 3-oxoacyl-CoA reductase; matches the UniProt-curated catalytic activity. Supporting Evidence: file:yeast/IFA38/IFA38-uniprot.txt Reaction=a very-long-chain (3R)-3-hydroxyacyl-CoA + NADP(+) = a very- |
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Download this section (compressed HTML)Q: Does Ifa38 contribute structurally to Phs1 stability or activity within an elongase complex, given that ifa38 microsomes also show reduced 3-hydroxyacyl-CoA dehydration?
Q: What is the functional significance of the Ifa38-eIF2B interaction, and is it separable from VLCFA synthesis?
Experiment: Assay 3-ketoacyl-CoA reduction in ER membranes from ifa38, ayr1 and conditional ifa38 ayr1 strains, and reconstitute purified Ayr1 with Elo3, Phs1 and Tsc13 in proteoliposomes.
Hypothesis: Ayr1 is the only source of residual 3-ketoacyl-CoA reductase activity in ifa38 cells.
Microsomal beta-keto-reductase; contains oleate response element (ORE) sequence in the promoter region; mutants exhibit reduced VLCFA synthesis, accumulate high levels of dihydrosphingosine, phytosphingosine and medium-chain ceramides
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