dlp1 encodes subunit 2 of the fission yeast decaprenyl diphosphate synthase, a heterotetramer of two Dps1 and two Dlp1 subunits that condenses isopentenyl diphosphate onto farnesyl diphosphate to make all-trans-decaprenyl diphosphate, the C50 side chain of ubiquinone-10. Dlp1 belongs to the FPP/GGPP synthase family but is only weakly similar to Dps1 and to canonical prenyl diphosphate synthases; neither subunit is active alone. The dlp1 deletion lacks the enzyme activity and CoQ10 and shows the coq-mutant phenotypes of hydrogen peroxide sensitivity, need for antioxidants on minimal medium and sulfide overproduction. Dlp1 localises to mitochondria. Human PDSS2 does not complement the dlp1 deletion.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004659 prenyltransferase activity | IBA GO_REF:0000033 | TOO GENERAL | Summary: Generic prenyltransferase family activity; the specific decaprenyl-diphosphate synthase activity is annotated. Reason: True but uninformative. IBA from PAINT node PTN000243362 (PTHR12001, FPP/GGPP synthase family, GO_REF:0000033), whose seeds include dlp1. GO:0097269 all-trans-decaprenyl-diphosphate synthase activity, asserted in this review (contributes_to), is an is_a descendant of prenyltransferase activity: the activity requires the Dps1-Dlp1 heterotetramer and is lost in the dlp1 deletion (PMID:14519123). The node placement is not in question; same action as the dps1 and S. cerevisiae COQ1 rows. 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 The deletion mutant of dlp1 lacked the enzymatic activity of decaprenyl diphosphate synthase |
| 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 interaction with Dps1 is real and is captured informatively by GO:0032478 heterotetrameric polyprenyl diphosphate synthase complex and 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 dlp1 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 Dlp1 stabilises in a high-molecular-weight complex in an E. coli ispB mutant (PMID:20051244); a heterologous pairing with no more informative MF term. 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 dlp1 in mitochondria, in agreement with Dlp1-GFP/MitoTracker co-localisation (PMID:24911838). Direct evidence that cannot resolve the sub-compartment: 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; confirmed by GFP localisation of S. pombe Dlp1. Reason: IBA from PAINT node PTN000243365 (PTHR12001, GO_REF:0000033), of which dlp1 is a seed. The organelle claim holds: Dlp1-GFP expressed in the dlp1 deletion co-localises with MitoTracker-stained mitochondria (PMID:24911838), the basis of the curated UniProt location. The assay cannot resolve a sub-compartment, so the organelle term is the appropriate level. Supporting Evidence: PMID:24911838 signal generated by the Dlp1-GFP fusion protein expressed in the Ξdlp1 strain overlapped with that of mitochondria stained using MitoTracker Red FM dye file:SCHPO/dlp1/dlp1-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion |
| GO:0005739 mitochondrion | IDA PMID:24911838 Functional conservation of coenzyme Q biosynthetic genes amo... | ACCEPT | Summary: Mitochondrial localisation of the tagged protein. Reason: Dlp1-GFP expressed in the dlp1 deletion co-localises with MitoTracker-stained mitochondria (PMID:24911838). Whole-organelle co-staining: ACCEPT at the root organelle term. Supporting Evidence: PMID:24911838 the fluorescent signal generated by the Dlp1-GFP fusion protein expressed in the Ξdlp1 strain overlapped with that of mitochondria stained using MitoTracker Red FM dye |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt SubCell location mapping; consistent with GFP localisation of S. pombe Dlp1. Reason: UniProt SubCell mapping (GO_REF:0000044). Dlp1-GFP expressed in the dlp1 deletion strain co-localises with MitoTracker-stained mitochondria (PMID:24911838), and the curated UniProt location (mitochondrion) is tagged with that paper. The assay cannot resolve a sub-compartment, so the organelle term is the appropriate level. Supporting Evidence: PMID:24911838 signal generated by the Dlp1-GFP fusion protein expressed in the Ξdlp1 strain overlapped with that of mitochondria stained using MitoTracker Red FM dye file:SCHPO/dlp1/dlp1-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion |
| 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 dlp1 is a seed. Dlp1 is a subunit of the Dps1-Dlp1 decaprenyl diphosphate synthase that makes the decaprenyl side chain of CoQ10, so it does part of the work of ubiquinone biosynthesis (as a contributing subunit of the synthase). The dlp1 deletion lacks decaprenyl diphosphate synthase activity and makes no ubiquinone-10 (PMID:14519123), and the curated UniProt function is tagged with that paper. Supporting Evidence: file:SCHPO/dlp1/dlp1-uniprot.txt Supplies decaprenyl diphosphate, the precursor for the side chain of the isoprenoid quinones ubiquinone-10. PMID:14519123 The deletion mutant of dlp1 lacked the enzymatic activity of decaprenyl diphosphate synthase, did not produce ubiquinone-10 |
| GO:0006744 ubiquinone biosynthetic process | IDA PMID:14519123 Fission yeast decaprenyl diphosphate synthase consists of Dp... | ACCEPT | Summary: Dlp1, with Dps1, constitutes the decaprenyl diphosphate synthase that supplies the CoQ10 side chain (PMID:14519123). Reason: Co-expression of dps1 and dlp1 is required for ubiquinone-10 production in E. coli, and the dlp1 deletion makes no ubiquinone-10 (PMID:14519123). Dlp1 is a subunit of the side-chain synthase, so it does part of the work; core process. 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. PMID:14519123 The deletion mutant of dlp1 lacked the enzymatic activity of decaprenyl diphosphate synthase, did not produce ubiquinone-10 and had the typical ubiquinone-deficient S. pombe phenotypes |
| GO:0006744 ubiquinone biosynthetic process | IEA GO_REF:0000041 | ACCEPT | Summary: UniPathway mapping; consistent. Reason: UniPathway mapping (GO_REF:0000041). Dlp1 is a subunit of the Dps1-Dlp1 decaprenyl diphosphate synthase that makes the decaprenyl side chain of CoQ10, so it does part of the work of ubiquinone biosynthesis (as a contributing subunit of the synthase). The dlp1 deletion lacks decaprenyl diphosphate synthase activity and makes no ubiquinone-10 (PMID:14519123), and the curated UniProt function is tagged with that paper. Supporting Evidence: file:SCHPO/dlp1/dlp1-uniprot.txt Supplies decaprenyl diphosphate, the precursor for the side chain of the isoprenoid quinones ubiquinone-10. PMID:14519123 The deletion mutant of dlp1 lacked the enzymatic activity of decaprenyl diphosphate synthase, did not produce ubiquinone-10 |
| 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 is not a descendant of GO:0008299). Kept as non-core because ubiquinone biosynthesis carries the core process; consistent with the dps1 rows and the human PDSS1/PDSS2 reviews. IBA from PAINT node PTN000243362 (PTHR12001, GO_REF:0000033), seeded among others by dlp1. Supporting Evidence: file:SCHPO/dlp1/dlp1-uniprot.txt Supplies decaprenyl diphosphate, the precursor for the side chain of the isoprenoid quinones ubiquinone-10. PMID:14519123 The deletion mutant of dlp1 lacked the enzymatic activity of decaprenyl diphosphate synthase |
| GO:0008299 isoprenoid biosynthetic process | IMP 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 is not a descendant of GO:0008299). Kept as non-core because ubiquinone biosynthesis carries the core process; consistent with the dps1 rows and the human PDSS1/PDSS2 reviews. IMP: the dlp1 deletion lacks decaprenyl diphosphate synthase activity (PMID:14519123). Supporting Evidence: PMID:14519123 The deletion mutant of dlp1 lacked the enzymatic activity of decaprenyl diphosphate synthase, did not produce ubiquinone-10 and had the typical ubiquinone-deficient S. pombe phenotypes |
| 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 is not a descendant of GO:0008299). Kept as non-core because ubiquinone biosynthesis carries the core process; consistent with the dps1 rows and the human PDSS1/PDSS2 reviews. IMP: the dlp1 deletion lacks CoQ10 (PMID:24911838). 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/dlp1/dlp1-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: polyprenyl diphosphate synthase complex. The gene already carries the more specific heterotetrameric complex term, which the experimental evidence supports. Reason: IBA from PAINT node PTN000243365 (PTHR12001, GO_REF:0000033). Dps1 and Dlp1 form a heterotetrameric decaprenyl diphosphate synthase (PMID:14519123; UniProt SUBUNIT, tagged with that paper). The parent term is correct but less specific than GO:0032478 heterotetrameric polyprenyl diphosphate synthase complex, which this gene already carries by IPI. Same MODIFY as dps1 and human PDSS1/PDSS2. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000243365 Β· decaprenyl/solanesyl diphosphate synthase subunit PAINT node SUPPORTS TRANSFER The complex membership transfers correctly; the S. pombe complex is experimentally the heterotetrameric form, so the descendant term is preferred. Proposed replacements: heterotetrameric polyprenyl diphosphate synthase complex Supporting Evidence: PMID:14519123 Furthermore, the two proteins were shown to form a heterotetrameric complex. file:SCHPO/dlp1/dlp1-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 form a heterotetrameric complex and are both required for ubiquinone-10 synthesis (PMID:14519123); UniProt SUBUNIT records 2 dps1 plus 2 dlp1 subunits. Core complex. Supporting Evidence: PMID:14519123 Furthermore, the two proteins were shown to form a heterotetrameric complex. file:SCHPO/dlp1/dlp1-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 form a heterotetrameric complex and are both required for ubiquinone-10 synthesis (PMID:14519123); UniProt SUBUNIT records 2 dps1 plus 2 dlp1 subunits. Core complex. Supporting Evidence: PMID:14519123 Furthermore, the two proteins were shown to form a heterotetrameric complex. file:SCHPO/dlp1/dlp1-uniprot.txt Heterotetramer of 2 dps1 and 2 dlp1 subunits. |
| GO:0097269 all-trans-decaprenyl-diphosphate synthase activity | IDA PMID:14519123 Fission yeast decaprenyl diphosphate synthase consists of Dp... | ACCEPT | Summary: Dlp1 is needed together with Dps1 for DPS activity (contributes_to). Reason: Qualifier contributes_to: decaprenyl diphosphate synthase activity requires both subunits, and the dlp1 deletion lacks it (PMID:14519123). Dlp1 is the weakly homologous partner subunit; core function as a contributing subunit. Supporting Evidence: PMID:14519123 This indicates that both dps1 and dlp1 are required for the S. pombe enzymatic activity. PMID:14519123 The deletion mutant of dlp1 lacked the enzymatic activity of decaprenyl diphosphate synthase, did not produce ubiquinone-10 and had the typical ubiquinone-deficient S. pombe phenotypes |
| 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). The term is correct: the activity belongs to the Dps1-Dlp1 heterotetramer, both subunits are required, and the dlp1 deletion lacks it (PMID:14519123). The IDA row already records Dlp1's role as contributes_to. Supporting Evidence: PMID:14519123 This indicates that both dps1 and dlp1 are required for the S. pombe enzymatic activity. PMID:14519123 The deletion mutant of dlp1 lacked the enzymatic activity of decaprenyl diphosphate synthase, did not produce ubiquinone-10 file:SCHPO/dlp1/dlp1-uniprot.txt Supplies decaprenyl diphosphate, the precursor for the side chain of the isoprenoid quinones ubiquinone-10. |
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