Isc1 is the sole neutral sphingomyelinase-family enzyme of Saccharomyces cerevisiae, a Mg2+-dependent, phosphatidylserine-stimulated inositol phosphosphingolipid phospholipase C that hydrolyses the complex sphingolipids inositol phosphorylceramide (IPC), mannosyl-IPC and mannosyl-diinositol phosphorylceramide to ceramide (phytoceramide) plus the corresponding (mannosyl)inositol phosphate; it also cleaves sphingomyelin in vitro, although yeast does not make sphingomyelin. It is the only known enzyme of complex-sphingolipid catabolism in budding yeast. Isc1 is an integral membrane protein found in the ER during early growth that relocates to the mitochondrial outer membrane in late logarithmic/post-diauxic growth, where its activity rises and it generates mitochondrial alpha-hydroxylated very-long-chain phytoceramides needed for normal respiratory function. Isc1-derived ceramides also act as signals, for example in hydroxyurea resistance and the spindle assembly checkpoint through ceramide-activated PP2A (Cdc55). Its post-diauxic activation in vivo depends on the mitochondrial anionic phospholipids phosphatidylglycerol and cardiolipin (it is impaired in pgs1 mutants). Isc1 also contributes to Na+ and Li+ tolerance: isc1 mutants are salt sensitive because induction of the Ena1 cation-extrusion ATPase by Na+ and Li+ is reduced.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO IEA (IPR005135, endonuclease/exonuclease/phosphatase fold) for generic catalytic activity. True but uninformative; Isc1's activity is inositol phosphosphingolipid phospholipase C. Reason: Replace the uninformative root-level MF with the specific experimentally established activity. Proposed replacements: inositol phosphosphingolipid phospholipase activity Supporting Evidence: PMID:11006294 encodes IPS phospholipase C (IPS-PLC) |
| GO:0004767 sphingomyelin phosphodiesterase activity | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO IEA (IPR038772, neutral sphingomyelinase family) for sphingomyelin phosphodiesterase. Isc1 does hydrolyse SM in vitro (it was first detected as neutral SMase activity), but yeast lacks SM; the physiological substrates are inositol phosphosphingolipids. Reason: Demonstrated in vitro activity on a non-physiological substrate in yeast. Supporting Evidence: PMID:11006294 we observed that overexpression of ISC1 greatly increased neutral SMase activity, and this activity was dependent on the presence of phosphatidylserine |
| GO:0005739 mitochondrion | IDA PMID:14699160 Activation and localization of inositol phosphosphingolipid ... | ACCEPT | Summary: IDA (Vaena de Avalos et al. 2004) - confocal microscopy, differential centrifugation and sucrose-gradient mitochondria show Isc1 associated with mitochondria in late log phase. Supporting Evidence: PMID:14699160 Confocal microscopy revealed that the enzyme was predominantly in the ER during early growth but became associated with mitochondria in late logarithmic growth |
| GO:0005741 mitochondrial outer membrane | EXP PMID:14699160 Activation and localization of inositol phosphosphingolipid ... | ACCEPT | Summary: EXP for mitochondrial outer membrane from the 2004 localisation study; the sub-mitochondrial assignment is consistent with the 2007 fractionation data. Supporting Evidence: PMID:17880915 epitope-tagged Isc1p localized to the outer mitochondrial membrane as an integral membrane protein |
| GO:0005741 mitochondrial outer membrane | IDA PMID:17880915 Isc1 regulates sphingolipid metabolism in yeast mitochondria... | ACCEPT | Summary: IDA (Kitagaki et al. 2007) - western blots of highly purified mitochondrial membrane fractions place Isc1 in the outer membrane as an integral protein. Site of mitochondrial ceramide generation. Supporting Evidence: PMID:17880915 epitope-tagged Isc1p localized to the outer mitochondrial membrane as an integral membrane protein |
| GO:0005741 mitochondrial outer membrane | IEA GO_REF:0000044 | ACCEPT | Summary: IEA from UniProt subcellular location (SL-0172), based on the experimental studies. Correct. Supporting Evidence: file:yeast/ISC1/ISC1-uniprot.txt {ECO:0000269|PubMed:14699160}; Multi-pass membrane protein |
| GO:0005783 endoplasmic reticulum | HDA PMID:26928762 One library to make them all: streamlining the creation of y... | ACCEPT | Summary: HDA from the SWAT-GFP library (Weill et al. 2018). Consistent with the targeted finding that Isc1 is ER-resident in early growth. Supporting Evidence: PMID:14699160 the enzyme was predominantly in the ER during early growth |
| GO:0005783 endoplasmic reticulum | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA (PTN000273522) is_active_in ER, from S. pombe Css1 and Isc1 itself. Isc1 is ER-localised in early growth; reasonable family-level inference. Supporting Evidence: PMID:14699160 the enzyme was predominantly in the ER during early growth |
| GO:0005783 endoplasmic reticulum | IDA PMID:14699160 Activation and localization of inositol phosphosphingolipid ... | ACCEPT | Summary: IDA (2004 confocal/fractionation) - Isc1 predominantly in the ER during early logarithmic growth. Supporting Evidence: PMID:14699160 the enzyme was predominantly in the ER during early growth |
| GO:0005789 endoplasmic reticulum membrane | EXP PMID:14699160 Activation and localization of inositol phosphosphingolipid ... | ACCEPT | Summary: EXP for ER membrane; Isc1 is a multipass integral membrane protein located in the ER early in growth. Supporting Evidence: PMID:14699160 the enzyme was predominantly in the ER during early growth |
| GO:0005789 endoplasmic reticulum membrane | IEA GO_REF:0000044 | ACCEPT | Summary: IEA from UniProt subcellular location (SL-0097, ER membrane). Correct. Supporting Evidence: file:yeast/ISC1/ISC1-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum membrane |
| GO:0005829 cytosol | RCA GO_REF:0000123 | REMOVE | Summary: YeastPathways RCA (LIPASYN-PWY-1, phospholipid degradation) placing a phosphatidylcholine phospholipase C reaction in the cytosol. This rests on a mis-assignment of Isc1 to PC hydrolysis, and Isc1 is an integral membrane protein of the ER and mitochondrial outer membrane, not a cytosolic enzyme. Reason: Derived from an incorrect pathway assignment; contradicted by experimental membrane localisation. Supporting Evidence: PMID:17880915 epitope-tagged Isc1p localized to the outer mitochondrial membrane as an integral membrane protein |
| GO:0006665 sphingolipid metabolic process | IEA GO_REF:0000120 | TOO GENERAL | Summary: Combined IEA (ARBA, UniPathway UPA00222 sphingolipid metabolism). Correct but general; the specific process is complex-sphingolipid catabolism yielding ceramide. Supporting Evidence: PMID:11006294 This study identifies the first enzyme involved in catabolism of complex sphingolipids in S. cerevisiae. |
| GO:0009395 phospholipid catabolic process | RCA GO_REF:0000123 | MODIFY | Summary: YeastPathways RCA from the phospholipid degradation pathway (PC -> DAG + phosphocholine). Isc1 does not degrade glycerophospholipids; it degrades inositol phosphosphingolipids. The correct process (sphingolipid catabolic process, GO:0030149) is already annotated. Reason: Pathway assignment based on a non-existent PC-PLC activity; the real catabolic process is sphingolipid catabolism. Proposed replacements: sphingolipid catabolic process Supporting Evidence: PMID:11006294 This study identifies the first enzyme involved in catabolism of complex sphingolipids in S. cerevisiae. |
| GO:0016020 membrane | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA is_active_in membrane (PTN000273522). Isc1 is an integral membrane protein (ER and mitochondrial outer membrane); correct though general. Supporting Evidence: PMID:17880915 epitope-tagged Isc1p localized to the outer mitochondrial membrane as an integral membrane protein |
| GO:0030149 sphingolipid catabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA for sphingolipid catabolic process, from mammalian nSMases, S. pombe Css1 and Isc1. Correct. Supporting Evidence: PMID:11006294 This study identifies the first enzyme involved in catabolism of complex sphingolipids in S. cerevisiae. |
| GO:0030149 sphingolipid catabolic process | IDA PMID:11006294 Identification of ISC1 (YER019w) as inositol phosphosphingol... | ACCEPT | Summary: IDA (Sawai et al. 2000) - Isc1 hydrolyses IPC/MIPC/M(IP)2C, and isc1 deletion increases IPS levels in labelled cells. Core process. Supporting Evidence: PMID:11006294 Labeling yeast cells with [(3)H]dihydrosphingosine showed that IPS were increased in the deletion mutant cells. |
| GO:0034480 phosphatidylcholine phospholipase C activity | RCA GO_REF:0000123 | REMOVE | Summary: YeastPathways RCA assigning Isc1 to phosphatidylcholine phospholipase C (EC 3.1.4.3) in phospholipid degradation. No study reports PC hydrolysis by Isc1; it is a phospholipase C specific for inositol phosphosphingolipids (and SM in vitro). This is a YeastCyc misassignment of a sphingomyelinase-family enzyme to a glycerophospholipid reaction. Reason: Unsupported substrate assignment; Isc1 activity is on inositol phosphosphingolipids (GO:0052712). Supporting Evidence: PMID:11006294 Lysates of ISC1-overexpressing cells demonstrated very high PLC activities on IPS. |
| GO:0046513 ceramide biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA for ceramide biosynthetic process (PTN000273522). Isc1 produces ceramide by hydrolysing complex sphingolipids (the salvage/catabolic route rather than de novo synthesis); the GO term covers ceramide formation and is applied to nSMases generally. Supporting Evidence: PMID:17880915 These results suggest that Isc1p generates ceramide in mitochondria |
| GO:0046513 ceramide biosynthetic process | IMP PMID:17880915 Isc1 regulates sphingolipid metabolism in yeast mitochondria... | ACCEPT | Summary: IMP (Kitagaki et al. 2007) - isc1 mitochondria lose 93% of alpha-hydroxylated phytoceramide in post-diauxic phase. Supporting Evidence: PMID:17880915 These results suggest that Isc1p generates ceramide in mitochondria |
| GO:0046513 ceramide biosynthetic process | IMP PMID:23620586 Identification of C18:1-phytoceramide as the candidate lipid... | ACCEPT | Summary: IMP (Tripathi et al. 2013) - hydroxyurea-induced increases in phytoceramides are absent in isc1 cells. Supporting Evidence: PMID:23620586 Lipid analysis revealed that HU induced increases in phytoceramides in WT cells but not in isc1Ξ cells. |
| GO:0052712 inositol phosphosphingolipid phospholipase activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA (PTN000963383) for inositol phosphosphingolipid phospholipase activity, from S. pombe Css1 and Isc1. Correct; fungal-specific node. Supporting Evidence: PMID:11006294 encodes IPS phospholipase C (IPS-PLC) |
| GO:0052712 inositol phosphosphingolipid phospholipase activity | IDA PMID:11006294 Identification of ISC1 (YER019w) as inositol phosphosphingol... | ACCEPT | Summary: IDA (Sawai et al. 2000) - very high PLC activity on IPS in ISC1-overexpressing lysates; activity lost on deletion. Core molecular function. Supporting Evidence: PMID:11006294 Lysates of ISC1-overexpressing cells demonstrated very high PLC activities on IPS. Deletion of ISC1 eliminated endogenous IPS-PLC activities. |
| GO:0052712 inositol phosphosphingolipid phospholipase activity | IEA GO_REF:0000116 | ACCEPT | Summary: Rhea-based IEA (RHEA:55688, IPC hydrolysis). Correct. Supporting Evidence: file:yeast/ISC1/ISC1-uniprot.txt Xref=Rhea:RHEA:55688 |
| GO:0071944 cell periphery | HDA PMID:26928762 One library to make them all: streamlining the creation of y... | KEEP AS NON CORE | Summary: HDA from the SWAT-GFP library for cell periphery. Targeted studies place Isc1 in the ER and the mitochondrial outer membrane; a peripheral GFP signal could reflect cortical ER. Not supported as a functional site. Reason: Single high-throughput observation, likely cortical ER; not a documented site of activity. Supporting Evidence: PMID:26928762 One library to make them all: streamlining the creation of yeast libraries via a SWAp-Tag strategy. |
| GO:0071944 cell periphery | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: PAINT IBA is_active_in cell periphery, seeded by mammalian nSMase2 (SMPD3) and rat/S. pombe members. Plasma-membrane localisation is characteristic of the mammalian enzyme; S. cerevisiae Isc1 acts in the ER and mitochondria. Reason: Localisation largely inherited from mammalian members; at most a minor site for budding-yeast Isc1. Supporting Evidence: PMID:14699160 the enzyme was predominantly in the ER during early growth but became associated with mitochondria in late logarithmic growth |
| GO:0072711 cellular response to hydroxyurea | IMP PMID:23620586 Identification of C18:1-phytoceramide as the candidate lipid... | KEEP AS NON CORE | Summary: IMP (Tripathi et al. 2013) - isc1 cells are hydroxyurea-sensitive and HU induces Isc1 activity; C18:1-phytoceramide produced by Isc1 mediates resistance through Cdc55. A downstream signalling consequence of its ceramide product. Reason: Stress-response role mediated by the lipid product, not the enzymatic core. Supporting Evidence: PMID:23620586 HU launches a lipid pathway mediated by a specific sphingolipid, C18:1-phytoceramide, produced by Isc1 |
| GO:0090266 regulation of mitotic cell cycle spindle assembly checkpoint | IMP PMID:32205408 Yeast Sphingolipid Phospholipase Gene ISC1 Regulates the Spi... | KEEP AS NON CORE | Summary: IMP (Matmati et al. 2020) - ISC1 genetic interactions and checkpoint phenotypes link Isc1-derived ceramide/PP2A-Cdc55 to the spindle assembly checkpoint. Indirect regulatory role. Reason: Signalling consequence of ceramide production; pleiotropic. Supporting Evidence: PMID:32205408 We herein provide biochemical and biological evidence that ISC1 functions in the spindle assembly checkpoint. |
| GO:0120570 sphingophospholipase activity | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA IEA for sphingophospholipase activity, a parent of the specific inositol phosphosphingolipid phospholipase activity. Correct, less specific. Reason: Broad specificity. No single child term covers this activity, which acts on sphingomyelin and inositol phosphosphingolipids. This term is the lowest common ancestor of the child terms asserted here, so it states the range of the activity rather than repeating one of them. Supporting Evidence: PMID:11006294 encodes IPS phospholipase C (IPS-PLC) |
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Inositol phosphosphingolipid phospholipase C; hydrolyzes complex sphingolipids to produce ceramide; regulates the spindle assembly checkpoint upstream of PP2A-Cdc55; activates genes required for non-fermentable carbon source metabolism during the diauxic shift; mediates Na+ and Li+ halotolerance; activated by phosphatidylserine, cardiolipin and phosphatidylglycerol; mitochondrial outer membrane protein; ortholog of mammalian neutral sphingomyelinase type 2
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