dps1 encodes subunit 1 of the fission yeast decaprenyl diphosphate synthase, a heterotetramer of two Dps1 and two Dlp1 subunits. The enzyme is a trans-prenyltransferase of the FPP/GGPP synthase family that condenses seven isopentenyl diphosphate units onto farnesyl diphosphate to make all-trans-decaprenyl diphosphate, the C50 side chain of ubiquinone-10 (coenzyme Q10). Dps1 carries the conserved polyprenyl synthase motifs; Dlp1 is only weakly similar, yet both are required for activity. Loss of dps1 abolishes CoQ10 synthesis, giving the coq-mutant phenotypes of oxidative-stress sensitivity, sulfide overproduction and a need for antioxidants on minimal medium. Dps1 localises to mitochondria. Human PDSS1 complements the dps1 deletion.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004659 prenyltransferase activity | IBA GO_REF:0000033 | TOO GENERAL | Summary: Generic prenyltransferase family activity; the specific all-trans-decaprenyl-diphosphate synthase activity is annotated elsewhere in this review. Reason: True but uninformative. The IBA descends from PAINT node PTN000243362 (PTHR12001, FPP/GGPP synthase family, GO_REF:0000033), and dps1 sits inside that clade; the S. pombe dps1 disruptant lacks decaprenyl diphosphate synthase activity (PMID:9133618), so GO:0097269 all-trans-decaprenyl-diphosphate synthase activity, asserted in this review and an is_a descendant of prenyltransferase activity, entails this term. The node placement is not in question. Consistent with the TOO_GENERAL action on the same term in the S. cerevisiae COQ1 review. Supporting Evidence: PMID:9133618 This disruptant was not able to synthesize ubiquinone and had no detectable decaprenyl diphosphate synthase activity file:SCHPO/dps1/dps1-uniprot.txt PTHR12001; GERANYLGERANYL PYROPHOSPHATE SYNTHASE |
| GO:0004659 prenyltransferase activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: Generic prenyltransferase family activity; the specific all-trans-decaprenyl-diphosphate synthase activity is annotated elsewhere in this review. Reason: True but uninformative. This is an InterPro2GO mapping (GO_REF:0000002) from the polyprenyl synthase signature IPR000092; the S. pombe dps1 disruptant lacks decaprenyl diphosphate synthase activity (PMID:9133618), and the specific descendant GO:0097269, asserted in this review, entails this term. Supporting Evidence: PMID:9133618 This disruptant was not able to synthesize ubiquinone and had no detectable decaprenyl diphosphate synthase activity file:SCHPO/dps1/dps1-uniprot.txt IPR000092; Polyprenyl_synt. |
| GO:0005515 protein binding | IPI PMID:14519123 Fission yeast decaprenyl diphosphate synthase consists of Dp... | REMOVE | Summary: IPI with its heterotetramer partner (Dps1/Dlp1). Generic protein binding carries no functional information; the interaction itself is not in doubt and is captured in the complex membership and description. Reason: Bare protein binding is uninformative (protein-binding policy). The reported interaction, Dps1 with its Dlp1 partner subunit, is real and is captured informatively by GO:0032478 heterotetrameric polyprenyl diphosphate synthase complex and by contributes_to GO:0097269; removal does not dispute the interaction. Supporting Evidence: PMID:14519123 Furthermore, the two proteins were shown to form a heterotetrameric complex. |
| GO:0005515 protein binding | IPI PMID:20051244 A subunit of decaprenyl diphosphate synthase stabilizes octa... | REMOVE | Summary: IPI with E. coli IspB (octaprenyl diphosphate synthase) when dps1 is expressed heterologously in E. coli; a cross-species interaction. Reason: Bare protein binding is uninformative (protein-binding policy). The partner is E. coli IspB, which Dps1 (or Dlp1) stabilises in a high-molecular-weight complex when expressed in an E. coli ispB mutant (PMID:20051244); this is a heterologous, non-physiological pairing, and no more informative MF term applies. Removal does not dispute the observation. Supporting Evidence: PMID:20051244 IspB interacted with Dlp1 (or Dps1), forming a high-molecular weight complex that stabilized IspB, leading to full functionality. |
| GO:0005739 mitochondrion | HDA PMID:16823372 ORFeome cloning and global analysis of protein localization ... | ACCEPT | Summary: ORFeome YFP screen: mitochondrion. Reason: Genome-wide YFP-tagging screen (HDA) placed dps1 in mitochondria; this agrees with the single-gene Dps1-GFP/MitoTracker co-localisation (PMID:24911838). Per the organelle policy, direct evidence from an assay that cannot resolve the sub-compartment is ACCEPT at the root organelle term. Supporting Evidence: PMID:16823372 we determined the localization of 4,431 proteins, corresponding to approximately 90% of the fission yeast proteome, by tagging each ORF with the yellow fluorescent protein PMID:24911838 These results are consistent with those of a previous study [44] that examined the localization of 4,431 S. pombe proteins |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference of mitochondrial location. Reason: IBA from PAINT node PTN000243365 (PTHR12001, eukaryotic long-chain polyprenyl diphosphate synthase clade, GO_REF:0000033); dps1 is itself a seed of the node. The organelle claim holds: Dps1-GFP colocalises with mitochondria in S. pombe (PMID:24911838), the basis of the curated UniProt location. Whole-organelle co-staining does not resolve the sub-compartment, so the row stays at the root organelle term. Supporting Evidence: PMID:24911838 The Dps1, Ppt1/Coq2, Coq3, Coq4, Coq5, Coq6, Coq7, Coq8, and Coq9 GFP fusion proteins also localized to the mitochondria |
| GO:0005739 mitochondrion | IDA PMID:24911838 Functional conservation of coenzyme Q biosynthetic genes amo... | ACCEPT | Summary: Mitochondrial localisation of the tagged protein. Reason: Dps1-GFP expressed in the dps1 deletion co-localises with MitoTracker-stained mitochondria (PMID:24911838). Whole-organelle co-staining is ACCEPT at the root organelle term under the organelle policy. Supporting Evidence: PMID:24911838 The Dps1, Ppt1/Coq2, Coq3, Coq4, Coq5, Coq6, Coq7, Coq8, and Coq9 GFP fusion proteins also localized to the mitochondria PMID:24911838 The results presented here demonstrate that all of the S. pombe Coq proteins localize to mitochondria, indicating that CoQ biosynthesis occurs in these cellular compartments. |
| GO:0005739 mitochondrion | IEA GO_REF:0000120 | ACCEPT | Summary: UniProt SubCell/ARBA location mapping (GO_REF:0000120); consistent with experimental localisation. Reason: Dps1-GFP colocalises with mitochondria in S. pombe (PMID:24911838), which UniProt records as experimental (ECO:0000269). The organelle claim holds; that paper's whole-organelle co-staining does not resolve the sub-compartment. Supporting Evidence: PMID:24911838 The Dps1, Ppt1/Coq2, Coq3, Coq4, Coq5, Coq6, Coq7, Coq8, and Coq9 GFP fusion proteins also localized to the mitochondria file:SCHPO/dps1/dps1-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:24911838}. |
| GO:0006744 ubiquinone biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference; ubiquinone biosynthesis step. Reason: IBA from PAINT node PTN000243365 (PTHR12001, GO_REF:0000033), of which dps1 is a seed. Dps1 does part of the work of ubiquinone biosynthesis: it is a subunit of the enzyme that makes the decaprenyl side chain. S. pombe dps1 disruption abolishes ubiquinone synthesis and decaprenyl diphosphate synthase activity (PMID:9133618), and both dps1 and dlp1 are needed for the activity (PMID:14519123). Supporting Evidence: PMID:9133618 This disruptant was not able to synthesize ubiquinone and had no detectable decaprenyl diphosphate synthase activity PMID:14519123 both dps1 and dlp1 are required for the S. pombe enzymatic activity |
| GO:0006744 ubiquinone biosynthetic process | IDA PMID:14519123 Fission yeast decaprenyl diphosphate synthase consists of Dp... | ACCEPT | Summary: Dps1, with Dlp1, constitutes the decaprenyl diphosphate synthase that supplies the CoQ10 side chain (ComplexPortal annotation from PMID:14519123). Reason: Co-expression of dps1 and dlp1 is required, and sufficient, to make ubiquinone-10 in E. coli, and the two form the heterotetrameric decaprenyl diphosphate synthase (PMID:14519123). Dps1 performs a step of ubiquinone biosynthesis (side-chain synthesis); core process. Supporting Evidence: PMID:14519123 Here we show that decaprenyl diphosphate synthase from Schizosaccharomyces pombe is comprised of a novel protein named Dlp1 acting in partnership with Dps1. PMID:14519123 We showed that the two proteins must be present simultaneously in Escherichia coli transformants before ubiquinone-10, which is produced by S. pombe but not by E. coli, is generated. |
| GO:0006744 ubiquinone biosynthetic process | IEA GO_REF:0000041 | ACCEPT | Summary: Mapping; consistent. Reason: UniPathway mapping (GO_REF:0000041, UPA00232). Confirmed by gene-specific evidence: dps1 disruption abolishes ubiquinone synthesis and decaprenyl diphosphate synthase activity (PMID:9133618), and both dps1 and dlp1 are needed for the activity (PMID:14519123). Supporting Evidence: PMID:9133618 This disruptant was not able to synthesize ubiquinone and had no detectable decaprenyl diphosphate synthase activity PMID:14519123 both dps1 and dlp1 are required for the S. pombe enzymatic activity |
| GO:0006744 ubiquinone biosynthetic process | IMP PMID:9133618 Analysis of the decaprenyl diphosphate synthase (dps) gene i... | ACCEPT | Summary: dps1 disruption abolishes ubiquinone-10 production. Reason: The S. pombe dps1 disruptant cannot synthesise ubiquinone and lacks decaprenyl diphosphate synthase activity (PMID:9133618); confirmed by the dps1 deletion in PMID:24911838. Core process. Supporting Evidence: PMID:9133618 This disruptant was not able to synthesize ubiquinone and had no detectable decaprenyl diphosphate synthase activity, indicating that the dps gene is unique and responsible for ubiquinone biosynthesis. |
| GO:0008299 isoprenoid biosynthetic process | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Broad but accurate process: the Dps1-Dlp1 enzyme synthesises decaprenyl diphosphate, an isoprenoid (the CoQ10 side-chain precursor). Reason: The term is true and no more specific GO process exists for decaprenyl diphosphate biosynthesis (GO:0006744 ubiquinone biosynthetic process is not a descendant of GO:0008299, so TOO_GENERAL does not apply). Kept as non-core because ubiquinone biosynthesis carries the core process; consistent with the dlp1 rows for this term and with the human PDSS1/PDSS2 reviews. The IBA descends from PAINT node PTN000243362 (PTHR12001, GO_REF:0000033), whose seeds include dps1. Supporting Evidence: PMID:9133618 This disruptant was not able to synthesize ubiquinone and had no detectable decaprenyl diphosphate synthase activity file:SCHPO/dps1/dps1-uniprot.txt Supplies decaprenyl diphosphate, the precursor for the side chain of the isoprenoid quinones ubiquinone-10. |
| GO:0008299 isoprenoid biosynthetic process | IDA PMID:14519123 Fission yeast decaprenyl diphosphate synthase consists of Dp... | KEEP AS NON CORE | Summary: Broad but accurate process: the Dps1-Dlp1 enzyme synthesises decaprenyl diphosphate, an isoprenoid (the CoQ10 side-chain precursor). Reason: The term is true and no more specific GO process exists for decaprenyl diphosphate biosynthesis (GO:0006744 ubiquinone biosynthetic process is not a descendant of GO:0008299, so TOO_GENERAL does not apply). Kept as non-core because ubiquinone biosynthesis carries the core process; consistent with the dlp1 rows for this term and with the human PDSS1/PDSS2 reviews. The IDA (PMID:14519123) rests on the reconstitution of decaprenyl diphosphate synthesis from Dps1 and Dlp1. Supporting Evidence: PMID:14519123 We showed that the two proteins must be present simultaneously in Escherichia coli transformants before ubiquinone-10, which is produced by S. pombe but not by E. coli, is generated. |
| GO:0008299 isoprenoid biosynthetic process | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Broad but accurate process: the Dps1-Dlp1 enzyme synthesises decaprenyl diphosphate, an isoprenoid (the CoQ10 side-chain precursor). Reason: The term is true and no more specific GO process exists for decaprenyl diphosphate biosynthesis (GO:0006744 ubiquinone biosynthetic process is not a descendant of GO:0008299, so TOO_GENERAL does not apply). Kept as non-core because ubiquinone biosynthesis carries the core process; consistent with the dlp1 rows for this term and with the human PDSS1/PDSS2 reviews. Electronic InterPro2GO mapping (GO_REF:0000002) from IPR000092. Supporting Evidence: PMID:9133618 This disruptant was not able to synthesize ubiquinone and had no detectable decaprenyl diphosphate synthase activity file:SCHPO/dps1/dps1-uniprot.txt Supplies decaprenyl diphosphate, the precursor for the side chain of the isoprenoid quinones ubiquinone-10. |
| GO:0008299 isoprenoid biosynthetic process | IMP PMID:24911838 Functional conservation of coenzyme Q biosynthetic genes amo... | KEEP AS NON CORE | Summary: Broad but accurate process: the Dps1-Dlp1 enzyme synthesises decaprenyl diphosphate, an isoprenoid (the CoQ10 side-chain precursor). Reason: The term is true and no more specific GO process exists for decaprenyl diphosphate biosynthesis (GO:0006744 ubiquinone biosynthetic process is not a descendant of GO:0008299, so TOO_GENERAL does not apply). Kept as non-core because ubiquinone biosynthesis carries the core process; consistent with the dlp1 rows for this term and with the human PDSS1/PDSS2 reviews. The IMP (PMID:24911838) rests on loss of CoQ10 in the dps1 deletion. Supporting Evidence: PMID:24911838 Here, we expand these findings by identifying ten genes (dps1, dlp1, ppt1, and coq3-9) that are required for CoQ synthesis. file:SCHPO/dps1/dps1-uniprot.txt Supplies decaprenyl diphosphate, the precursor for the side chain of the isoprenoid quinones ubiquinone-10. |
| GO:0032476 polyprenyl diphosphate synthase complex | IBA GO_REF:0000033 | MODIFY | Summary: PAINT inference of polyprenyl diphosphate synthase complex; the specific heterotetrameric complex is supported. Reason: IBA from PAINT node PTN000243365 (PTHR12001, GO_REF:0000033). The term is correct but general: dps1 and dlp1 form a heterotetrameric decaprenyl diphosphate synthase (PMID:14519123; UniProt SUBUNIT, ECO:0000269), and the gene already carries the specific child GO:0032478 heterotetrameric polyprenyl diphosphate synthase complex by IPI. Same MODIFY as the human PDSS1/PDSS2 reviews. Propagation Review Root cause: NO FAILURE CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000243365 SUPPORTS TRANSFER The node correctly places dps1 in a polyprenyl diphosphate synthase complex; the gene-specific IPI evidence refines it to the heterotetrameric complex. Proposed replacements: heterotetrameric polyprenyl diphosphate synthase complex Supporting Evidence: PMID:14519123 the two proteins were shown to form a heterotetrameric complex file:SCHPO/dps1/dps1-uniprot.txt Heterotetramer of 2 dps1 and 2 dlp1 subunits. |
| GO:0032478 heterotetrameric polyprenyl diphosphate synthase complex | IPI PMID:14519123 Fission yeast decaprenyl diphosphate synthase consists of Dp... | ACCEPT | Summary: Dps1 and Dlp1 form a heterotetrameric decaprenyl diphosphate synthase. Reason: Dps1 and Dlp1 together make ubiquinone-10 when co-expressed and form a heterotetrameric complex (PMID:14519123); UniProt SUBUNIT records a heterotetramer of 2 dps1 and 2 dlp1 subunits. Core complex. Supporting Evidence: PMID:14519123 Furthermore, the two proteins were shown to form a heterotetrameric complex. file:SCHPO/dps1/dps1-uniprot.txt Heterotetramer of 2 dps1 and 2 dlp1 subunits. |
| GO:0032478 heterotetrameric polyprenyl diphosphate synthase complex | IPI PMID:14519123 Fission yeast decaprenyl diphosphate synthase consists of Dp... | ACCEPT | Summary: Dps1 and Dlp1 form a heterotetrameric decaprenyl diphosphate synthase. Reason: Dps1 and Dlp1 together make ubiquinone-10 when co-expressed and form a heterotetrameric complex (PMID:14519123); UniProt SUBUNIT records a heterotetramer of 2 dps1 and 2 dlp1 subunits. Core complex. Supporting Evidence: PMID:14519123 Furthermore, the two proteins were shown to form a heterotetrameric complex. file:SCHPO/dps1/dps1-uniprot.txt Heterotetramer of 2 dps1 and 2 dlp1 subunits. |
| GO:0045337 trans, trans-farnesyl diphosphate biosynthetic process | IMP PMID:9133618 Analysis of the decaprenyl diphosphate synthase (dps) gene i... | MARK AS OVER ANNOTATED | Summary: IMP for trans,trans-farnesyl diphosphate biosynthesis from the dps disruptant. Dps1 uses FPP as its allylic primer and extends it to decaprenyl diphosphate; it does not form FPP. Reason: By definition GO:0045337 is the formation of 2-trans,6-trans-farnesyl diphosphate. In the enzyme's curated reaction FPP is the substrate, not the product, and the phenotypes reported for the disruptant (no ubiquinone, no decaprenyl diphosphate synthase activity; PMID:9133618) say nothing about FPP formation, which in S. pombe belongs to the FPP synthase. The paper's full text is not cached, so the curator's reading cannot be checked fully, and the row is not removed; it is marked as an over-annotation that probably reflects the product's use of FPP. The correct process, GO:0006744, is accepted, and GO:0008299 covers isoprenoid chain elongation. Supporting Evidence: PMID:9133618 This disruptant was not able to synthesize ubiquinone and had no detectable decaprenyl diphosphate synthase activity file:SCHPO/dps1/dps1-uniprot.txt Reaction=7 isopentenyl diphosphate + (2E,6E)-farnesyl diphosphate = all-trans-decaprenyl diphosphate + 7 diphosphate |
| GO:0097269 all-trans-decaprenyl-diphosphate synthase activity | IEA GO_REF:0000120 | ACCEPT | Summary: EC mapping; decaprenyl diphosphate synthase. Reason: EC/Rhea mapping (GO_REF:0000120, EC 2.5.1.91). Confirmed experimentally: decaprenyl diphosphate synthase activity is lost in the S. pombe dps1 disruptant (PMID:9133618) and requires both dps1 and dlp1 (PMID:14519123). Core function. Supporting Evidence: PMID:9133618 This disruptant was not able to synthesize ubiquinone and had no detectable decaprenyl diphosphate synthase activity PMID:14519123 both dps1 and dlp1 are required for the S. pombe enzymatic activity |
| GO:0097269 all-trans-decaprenyl-diphosphate synthase activity | IMP PMID:9133618 Analysis of the decaprenyl diphosphate synthase (dps) gene i... | ACCEPT | Summary: dps1 disruption abolishes decaprenyl (UQ-10 side chain) synthesis. Reason: The dps1 disruptant has no detectable decaprenyl diphosphate synthase activity (PMID:9133618), and both dps1 and dlp1 are needed for the activity (PMID:14519123). Dps1 is the canonical FPP/GGPP-synthase-family catalytic subunit of the heterotetramer; core function. Supporting Evidence: PMID:9133618 This disruptant was not able to synthesize ubiquinone and had no detectable decaprenyl diphosphate synthase activity PMID:14519123 This indicates that both dps1 and dlp1 are required for the S. pombe enzymatic activity. |
| GO:0120531 prenyl diphosphate synthase activity | IEA GO_REF:0000117 | TOO GENERAL | Summary: Generic prenyl diphosphate synthase; the specific all-trans-decaprenyl-diphosphate synthase activity is annotated elsewhere in this review. Reason: True but uninformative. ARBA machine-learning rule (GO_REF:0000117). GO:0097269 all-trans-decaprenyl-diphosphate synthase activity, asserted in this review, is an is_a descendant of prenyl diphosphate synthase activity; the S. pombe dps1 disruptant lacks decaprenyl diphosphate synthase activity (PMID:9133618). Supporting Evidence: PMID:9133618 This disruptant was not able to synthesize ubiquinone and had no detectable decaprenyl diphosphate synthase activity file:SCHPO/dps1/dps1-uniprot.txt Reaction=7 isopentenyl diphosphate + (2E,6E)-farnesyl diphosphate = all-trans-decaprenyl diphosphate + 7 diphosphate |
| GO:1901663 quinone biosynthetic process | IEA GO_REF:0000117 | TOO GENERAL | Summary: Broad parent of ubiquinone biosynthetic process, which is asserted in this review. Reason: True but uninformative. ARBA rule (GO_REF:0000117). GO:0006744 ubiquinone biosynthetic process, asserted in this review, is an is_a descendant of quinone biosynthetic process; the S. pombe dps1 disruptant cannot make ubiquinone (PMID:9133618). Supporting Evidence: PMID:9133618 This disruptant was not able to synthesize ubiquinone and had no detectable decaprenyl diphosphate synthase activity file:SCHPO/dps1/dps1-uniprot.txt Supplies decaprenyl diphosphate, the precursor for the side chain of the isoprenoid quinones ubiquinone-10. |
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