PHS1 (YJL097W) encodes the very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase of S. cerevisiae, the founding member of the HACD/PTPLA family (orthologous to mammalian HACD1-4). This essential six-pass endoplasmic reticulum membrane protein, with both termini facing the cytosol, catalyses the third of the four reactions of the ER fatty acid elongation cycle, dehydrating the (3R)-3-hydroxyacyl-CoA produced by Ifa38 to trans-2,3-enoyl-CoA, which Tsc13 then reduces. Conserved residues Tyr-149 and Glu-156 are indispensable and Arg83 and Gly152 contribute directly to catalysis. Phs1 functions with the Elo2/Elo3 condensing enzymes to produce C20-C26 very long-chain fatty acids; depletion impairs elongation and the conversion of ceramide to inositol phosphorylceramide. High-throughput GFP surveys also report a vacuolar membrane signal.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000324 fungal-type vacuole | HDA PMID:14562095 Global analysis of protein localization in budding yeast. | KEEP AS NON CORE | Summary: Huh et al. 2003 GFP survey; Phs1-GFP was assigned a vacuolar call in addition to ER. Reason: Phs1 is a six-pass ER membrane enzyme whose topology and activity were characterised in ER membranes, and the elongation cycle is ER-bound. Vacuolar GFP signal in high-throughput surveys may reflect ER-vacuole/nucleus-vacuole contact sites or turnover of the fusion protein. Kept as non-core rather than removed because these are experimental calls whose primary images were not inspected. Supporting Evidence: PMID:14562095 We classify these proteins, representing 75% of the yeast proteome, into 22 distinct subcellular localization categories file:yeast/PHS1/PHS1-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum membrane |
| GO:0000324 fungal-type vacuole | HDA PMID:14690591 Assigning function to yeast proteins by integration of techn... | KEEP AS NON CORE | Summary: Hazbun et al. 2003 localised uncharacterised essential ORFs (including YJL097W/Phs1) by fluorescence microscopy; vacuolar call. Reason: Phs1 is a six-pass ER membrane enzyme whose topology and activity were characterised in ER membranes, and the elongation cycle is ER-bound. Vacuolar GFP signal in high-throughput surveys may reflect ER-vacuole/nucleus-vacuole contact sites or turnover of the fusion protein. Kept as non-core rather than removed because these are experimental calls whose primary images were not inspected. Supporting Evidence: PMID:14690591 fluorescence microscopy to localize the proteins |
| GO:0000324 fungal-type vacuole | IDA PMID:23708375 Organelle acidification is important for localisation of vac... | KEEP AS NON CORE | Summary: Matsumoto et al. 2013 examined GFP-fusions of proteins predicted to be vacuolar, including Phs1 (curated IDA), and their dependence on V-ATPase acidification for vacuolar localisation. Reason: Phs1 is a six-pass ER membrane enzyme whose topology and activity were characterised in ER membranes, and the elongation cycle is ER-bound. Vacuolar GFP signal in high-throughput surveys may reflect ER-vacuole/nucleus-vacuole contact sites or turnover of the fusion protein. Kept as non-core rather than removed because these are experimental calls whose primary images were not inspected. Supporting Evidence: PMID:23708375 we examined the localisation of GFP-fused proteins that were predicted to localise in the vacuolar lumen or on the vacuolar membrane |
| GO:0000329 fungal-type vacuole membrane | HDA PMID:14690591 Assigning function to yeast proteins by integration of techn... | KEEP AS NON CORE | Summary: Hazbun et al. 2003 high-throughput microscopy call of vacuole membrane for Phs1. Reason: Phs1 is a six-pass ER membrane enzyme whose topology and activity were characterised in ER membranes, and the elongation cycle is ER-bound. Vacuolar GFP signal in high-throughput surveys may reflect ER-vacuole/nucleus-vacuole contact sites or turnover of the fusion protein. Kept as non-core rather than removed because these are experimental calls whose primary images were not inspected. Supporting Evidence: PMID:14690591 fluorescence microscopy to localize the proteins |
| GO:0004300 enoyl-CoA hydratase activity | IDA PMID:18272525 Membrane topology and essential amino acid residues of Phs1,... | MODIFY | Summary: Kihara et al. 2008 assayed Phs1 3-hydroxyacyl-CoA dehydratase activity (the reverse of enoyl-CoA hydration). In GO, enoyl-CoA hydratase activity is an ancestor of the VLC (3R)-3-hydroxyacyl-CoA dehydratase term, so this is correct but much less specific; its definition is centred on the (3S)-specific beta-oxidation crotonase reaction. Proposed replacements: very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase activity Supporting Evidence: PMID:18272525 Yeast Phs1 is the 3-hydroxyacyl-CoA dehydratase that catalyzes the third reaction of the four-step cycle in the elongation of very long-chain fatty acids (VLCFAs) |
| GO:0004300 enoyl-CoA hydratase activity | RCA GO_REF:0000123 | MODIFY | Summary: YeastPathways PWY-5080-1 assigns the dehydration step (EC 4.2.1.17 in YeastCyc) to Phs1. The step is right; EC 4.2.1.17 is the (3S) beta-oxidation enoyl-CoA hydratase, whereas Phs1 acts on (3R)-3-hydroxyacyl-CoA (EC 4.2.1.134). Proposed replacements: very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase activity Supporting Evidence: PMID:18272525 Yeast Phs1 is the 3-hydroxyacyl-CoA dehydratase that catalyzes the third reaction of the four-step cycle in the elongation of very long-chain fatty acids (VLCFAs) file:yeast/PHS1/PHS1-uniprot.txt Reaction=a very-long-chain (3R)-3-hydroxyacyl-CoA = a very-long-chain |
| GO:0005774 vacuolar membrane | EXP PMID:14562095 Global analysis of protein localization in budding yeast. | KEEP AS NON CORE | Summary: UniProt-curated EXP for vacuole membrane citing the Huh et al. 2003 GFP survey. Reason: Phs1 is a six-pass ER membrane enzyme whose topology and activity were characterised in ER membranes, and the elongation cycle is ER-bound. Vacuolar GFP signal in high-throughput surveys may reflect ER-vacuole/nucleus-vacuole contact sites or turnover of the fusion protein. Kept as non-core rather than removed because these are experimental calls whose primary images were not inspected. Supporting Evidence: PMID:14562095 We classify these proteins, representing 75% of the yeast proteome, into 22 distinct subcellular localization categories file:yeast/PHS1/PHS1-uniprot.txt Vacuole membrane {ECO:0000269|PubMed:14562095} |
| GO:0005774 vacuolar membrane | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: UniProt subcellular-location keyword mapping (SL-0271 Vacuole membrane) derived from the Huh et al. call. Reason: Phs1 is a six-pass ER membrane enzyme whose topology and activity were characterised in ER membranes, and the elongation cycle is ER-bound. Vacuolar GFP signal in high-throughput surveys may reflect ER-vacuole/nucleus-vacuole contact sites or turnover of the fusion protein. Kept as non-core rather than removed because these are experimental calls whose primary images were not inspected. Supporting Evidence: file:yeast/PHS1/PHS1-uniprot.txt Vacuole membrane {ECO:0000269|PubMed:14562095} |
| GO:0005783 endoplasmic reticulum | HDA PMID:14562095 Global analysis of protein localization in budding yeast. | ACCEPT | Summary: Huh et al. 2003 GFP survey scored Phs1-GFP at the ER; consistent with its ER-bound enzymatic role. Supporting Evidence: PMID:14562095 We classify these proteins, representing 75% of the yeast proteome, into 22 distinct subcellular localization categories file:yeast/PHS1/PHS1-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum membrane |
| GO:0005783 endoplasmic reticulum | HDA PMID:26928762 One library to make them all: streamlining the creation of y... | ACCEPT | Summary: Yofe et al. 2016 SWAT N-terminal GFP library of endomembrane proteins localised Phs1 to the ER. Supporting Evidence: PMID:26928762 we constructed and investigated a library of ∼1,800 strains carrying SWAT-GFP modules at the amino termini of endomembrane proteins |
| GO:0005789 endoplasmic reticulum membrane | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA from the HACD/PTPLA family node PTN000112207; all characterised members (yeast Phs1, mammalian HACD1-4) are ER membrane dehydratases. Supporting Evidence: PMID:18272525 Our results suggest that Phs1 is a membrane-spanning protein that traverses the membrane six times and has an N terminus and C terminus facing the cytosol file:yeast/PHS1/PHS1-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum membrane |
| GO:0005789 endoplasmic reticulum membrane | IDA PMID:18272525 Membrane topology and essential amino acid residues of Phs1,... | ACCEPT | Summary: Kihara et al. 2008 determined Phs1 membrane topology (six transmembrane segments, N- and C-termini cytosolic) in the ER and measured its activity in membranes. Supporting Evidence: PMID:18272525 Our results suggest that Phs1 is a membrane-spanning protein that traverses the membrane six times and has an N terminus and C terminus facing the cytosol file:yeast/PHS1/PHS1-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum membrane |
| GO:0005789 endoplasmic reticulum membrane | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location keyword mapping (SL-0097) from the experimental ER membrane statement. Supporting Evidence: file:yeast/PHS1/PHS1-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum membrane |
| GO:0005829 cytosol | RCA GO_REF:0000123 | REMOVE | Summary: YeastPathways PWY-5080-1 conversion default 'is_active_in cytosol'. Phs1 is a six-pass integral ER membrane protein. Reason: Computational compartment default contradicted by the experimentally determined ER membrane topology. Supporting Evidence: PMID:18272525 Our results suggest that Phs1 is a membrane-spanning protein that traverses the membrane six times and has an N terminus and C terminus facing the cytosol file:yeast/PHS1/PHS1-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum membrane |
| GO:0005829 cytosol | RCA GO_REF:0000123 | REMOVE | Summary: YeastPathways PWY-5177 (glutaryl-CoA degradation) 'is_active_in cytosol'. Both the pathway assignment (see below) and the soluble cytosolic location are wrong for Phs1. Reason: Phs1 is an integral ER membrane protein; the PWY-5177 assignment is a YeastCyc reaction-matching artefact. Supporting Evidence: PMID:18272525 Our results suggest that Phs1 is a membrane-spanning protein that traverses the membrane six times and has an N terminus and C terminus facing the cytosol file:yeast/PHS1/PHS1-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 Phs1 acts specifically in VLCFA elongation. Proposed replacements: very long-chain fatty acid biosynthetic process Supporting Evidence: PMID:18272525 Yeast Phs1 is the 3-hydroxyacyl-CoA dehydratase that catalyzes the third reaction of the four-step cycle in the elongation of very long-chain fatty acids (VLCFAs) |
| GO:0007034 vacuolar transport | IMP PMID:16943325 A survey of essential gene function in the yeast cell divisi... | MARK AS OVER ANNOTATED | Summary: Yu et al. 2006 tetO7 promoter-shutoff screen predicted PHS1 as a protein-trafficking gene from cell-cycle/DNA-content phenotypes. Trafficking defects on Phs1 depletion are expected consequences of VLCFA/sphingolipid loss; Phs1 itself performs no transport step. Reason: Indirect lipid-dependent phenotype from a large-scale screen; Phs1 does not participate in vacuolar transport. Kept as over-annotation (IMP) rather than removed. Supporting Evidence: PMID:16943325 we identified four new genes involved in protein trafficking (NUS1, PHS1, PGA2, PGA3) PMID:18272525 reduced Phs1 levels result in significant impairment of the conversion of ceramide to inositol phosphorylceramide |
| GO:0018812 3-hydroxyacyl-CoA dehydratase activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA (PTN000112207) for 3-hydroxyacyl-CoA dehydratase activity, the defining HACD-family activity; correct for Phs1 (VLC-specific child term also annotated). Supporting Evidence: PMID:18272525 Yeast Phs1 is the 3-hydroxyacyl-CoA dehydratase that catalyzes the third reaction of the four-step cycle in the elongation of very long-chain fatty acids (VLCFAs) PMID:23416297 All mutants exhibited reduced Phs1 activity. |
| GO:0018812 3-hydroxyacyl-CoA dehydratase activity | IMP PMID:23416297 Identification of residues important for the catalysis, stru... | ACCEPT | Summary: Yazawa et al. 2013 Ala-scanning of conserved residues: all mutants reduced Phs1 dehydratase activity and kinetics implicate Arg83 and Gly152 in catalysis. Supporting Evidence: PMID:23416297 All mutants exhibited reduced Phs1 activity. PMID:23416297 The enzyme kinetics study implicated the direct involvement of the Arg83 and Gly152 residues in the catalytic process. |
| GO:0018812 3-hydroxyacyl-CoA dehydratase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways PWY-5177 (glutaryl-CoA degradation) attaches Phs1 to the crotonase-type step (3-hydroxybutanoyl-CoA dehydration). The general MF term is true of Phs1, but the pathway context is wrong: Phs1 is an ER VLCFA-elongation enzyme acting on (3R) long-chain substrates, with no evidence for short-chain activity in lysine/glutaryl-CoA catabolism. Accepted for the MF only; the PWY-5177 BP and cytosol rows are removed. Supporting Evidence: PMID:18272525 Yeast Phs1 is the 3-hydroxyacyl-CoA dehydratase that catalyzes the third reaction of the four-step cycle in the elongation of very long-chain fatty acids (VLCFAs) file:yeast/PHS1/PHS1-uniprot.txt Reaction=a very-long-chain (3R)-3-hydroxyacyl-CoA = a very-long-chain |
| GO:0030148 sphingolipid biosynthetic process | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: PAINT IBA for sphingolipid biosynthesis. Phs1 supplies VLCFA-CoA used for C26-ceramide; it catalyses no sphingolipid-forming reaction. Supporting Evidence: PMID:18272525 reduced Phs1 levels result in significant impairment of the conversion of ceramide to inositol phosphorylceramide |
| GO:0030148 sphingolipid biosynthetic process | IMP PMID:18272525 Membrane topology and essential amino acid residues of Phs1,... | KEEP AS NON CORE | Summary: Kihara et al. 2008: reduced Phs1 levels impair conversion of ceramide to inositol phosphorylceramide. Upstream precursor-supply role. Supporting Evidence: PMID:18272525 reduced Phs1 levels result in significant impairment of the conversion of ceramide to inositol phosphorylceramide |
| GO:0030497 fatty acid elongation | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA (PTN000112207): dehydration is the third step of each elongation cycle; correct. Supporting Evidence: PMID:18272525 Yeast Phs1 is the 3-hydroxyacyl-CoA dehydratase that catalyzes the third reaction of the four-step cycle in the elongation of very long-chain fatty acids (VLCFAs) |
| GO:0030497 fatty acid elongation | IMP PMID:23416297 Identification of residues important for the catalysis, stru... | ACCEPT | Summary: Yazawa et al. 2013: the fatty acid elongation cycle was greatly inhibited in membranes carrying catalytic-residue mutants of Phs1. Supporting Evidence: PMID:23416297 The fatty acid elongation cycle was greatly inhibited in the R83A, R141A, and G152A mutant membranes. |
| GO:0042175 nuclear outer membrane-endoplasmic reticulum membrane network | HDA PMID:14690591 Assigning function to yeast proteins by integration of techn... | ACCEPT | Summary: Hazbun et al. 2003 microscopy call of the nuclear envelope-ER network; consistent with ER residence. Supporting Evidence: PMID:14690591 fluorescence microscopy to localize the proteins file:yeast/PHS1/PHS1-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum membrane |
| GO:0042761 very long-chain fatty acid biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA (PTN000112207) for VLCFA biosynthesis; core process. Supporting Evidence: PMID:18272525 Yeast Phs1 is the 3-hydroxyacyl-CoA dehydratase that catalyzes the third reaction of the four-step cycle in the elongation of very long-chain fatty acids (VLCFAs) |
| GO:0042761 very long-chain fatty acid biosynthetic process | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways PWY-5080-1 assignment of the dehydration step to Phs1; correct. Supporting Evidence: PMID:18272525 Yeast Phs1 is the 3-hydroxyacyl-CoA dehydratase that catalyzes the third reaction of the four-step cycle in the elongation of very long-chain fatty acids (VLCFAs) 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:0046395 carboxylic acid catabolic process | RCA GO_REF:0000123 | REMOVE | Summary: YeastPathways PWY-5177 (glutaryl-CoA degradation) RCA. YeastCyc appears to have matched Phs1 to a generic 3-hydroxyacyl-CoA dehydration in this catabolic pathway; no evidence links Phs1, an ER VLCFA-elongation (anabolic) enzyme, to carboxylic acid catabolism. Reason: Pathway mis-assignment in YeastCyc; Phs1 functions in fatty acid elongation, not catabolism, and S. cerevisiae Phs1 has no reported short-chain or (3S) activity. Supporting Evidence: PMID:18272525 Yeast Phs1 is the 3-hydroxyacyl-CoA dehydratase that catalyzes the third reaction of the four-step cycle in the elongation of very long-chain fatty acids (VLCFAs) file:yeast/PHS1/PHS1-uniprot.txt Reaction=a very-long-chain (3R)-3-hydroxyacyl-CoA = a very-long-chain |
| GO:0080023 (2E)-enoyl-CoA hydratase activity | IEA GO_REF:0000116 | TOO GENERAL | Summary: IEA from Rhea (VLC (3R)-3-hydroxyacyl-CoA dehydration reactions) to (2E)-enoyl-CoA hydratase activity, the (3R)-stereospecific parent of the VLC dehydratase term. Correct stereochemistry; less specific than GO:0102158. Supporting Evidence: file:yeast/PHS1/PHS1-uniprot.txt Reaction=a very-long-chain (3R)-3-hydroxyacyl-CoA = a very-long-chain |
| GO:0102158 very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase activity | EXP PMID:17719544 A molecular caliper mechanism for determining very long-chai... | ACCEPT | Summary: Denic and Weissman 2007 reconstituted the elongation cycle from purified Elo, the novel dehydratase (Phs1) and two reductases. Supporting Evidence: 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:0102158 very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase activity | EXP PMID:18272525 Membrane topology and essential amino acid residues of Phs1,... | ACCEPT | Summary: Kihara et al. 2008 measured Phs1 3-hydroxyacyl-CoA dehydratase activity and identified indispensable residues Tyr-149 and Glu-156. Supporting Evidence: PMID:18272525 Yeast Phs1 is the 3-hydroxyacyl-CoA dehydratase that catalyzes the third reaction of the four-step cycle in the elongation of very long-chain fatty acids (VLCFAs) PMID:18272525 we identified six amino acid residues important in Phs1 function, two of which (Tyr-149 and Glu-156) are indispensable |
| GO:0102158 very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Combined IEA (RHEA:45812, EC 4.2.1.134) matching the UniProt-curated VLC (3R)-3-hydroxyacyl-CoA dehydratase reaction. Supporting Evidence: file:yeast/PHS1/PHS1-uniprot.txt Reaction=a very-long-chain (3R)-3-hydroxyacyl-CoA = a very-long-chain |
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Download this section (compressed HTML)Q: Is the vacuolar-membrane GFP signal reported for Phs1 a genuine second pool (e.g. at nucleus-vacuole junctions) or a consequence of C-terminal tagging/turnover?
Q: Does Phs1 have any activity toward short-chain or (3S)-3-hydroxyacyl-CoA substrates that would justify its YeastCyc placement in glutaryl-CoA degradation?
Experiment: Assay purified Phs1 in proteoliposomes with (3R)- and (3S)-3-hydroxybutanoyl-CoA, -hexadecanoyl-CoA and -eicosanoyl-CoA and quantify enoyl-CoA by LC-MS.
Hypothesis: Phs1 is stereospecific for (3R)-3-hydroxyacyl-CoA and inactive on short-chain substrates.
Essential 3-hydroxyacyl-CoA dehydratase of the ER membrane; involved in elongation of very long-chain fatty acids; evolutionarily conserved, similar to mammalian PTPLA and PTPLB; involved in sphingolipid biosynthesis and protein trafficking
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