coq4 encodes the fission yeast Coq4 protein of the COQ4 family, a zinc-binding peripheral protein on the matrix side of the mitochondrial inner membrane. By homology with COQ4 orthologs it catalyses the C1 oxidative decarboxylation of 4-hydroxy-3-methoxy-5-decaprenylbenzoate, the step that removes the carboxyl group of the ring precursor during coenzyme Q10 synthesis, and it organises the multi-subunit CoQ biosynthetic complex. Deletion of coq4 abolishes CoQ10 synthesis, and human or Arabidopsis COQ4 complements the deletion.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| 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 Coq4 in mitochondria, in agreement with the single-gene Coq4-GFP/MitoTracker result (PMID:24911838). Direct evidence from an assay 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. Reason: IBA from PAINT node PTN000308948 (PTHR12922, GO_REF:0000033). The PAINT mitochondrial inference is confirmed on the target itself - a Coq4-GFP fusion expressed in the deletion strain co-localised with MitoTracker-stained mitochondria (PMID:24911838) - and UniProt curates the location as mitochondrial inner membrane with experimental evidence; the organelle term is kept per the root-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 file:SCHPO/coq4/coq4-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion inner membrane |
| GO:0005739 mitochondrion | IDA PMID:24911838 Functional conservation of coenzyme Q biosynthetic genes amo... | ACCEPT | Summary: Mitochondrial localisation of the tagged protein. Reason: Coq4-GFP expressed in the corresponding deletion strain localises to MitoTracker-stained mitochondria (PMID:24911838). Whole-organelle co-staining: ACCEPT 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 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:0005743 mitochondrial inner membrane | EXP PMID:24911838 Functional conservation of coenzyme Q biosynthetic genes amo... | ACCEPT | Summary: PomBase EXP for inner-membrane location from the systematic S. pombe coq study. Reason: PMID:24911838 (full text cached) localises Coq4-GFP to mitochondria by co-staining without sub-mitochondrial fractionation; UniProt tags its inner-membrane line with this paper, PMID:16823372 and HAMAP MF_03111. The claim agrees with the S. cerevisiae ortholog, whose inner-membrane IDA rows are accepted in the COQ4 review, and with Coq4's role as an organiser of the membrane-associated CoQ synthome; accepted, not second-guessed. 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/coq4/coq4-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion inner membrane {ECO:0000255|HAMAP-Rule:MF_03111, ECO:0000269|PubMed:16823372, ECO:0000269|PubMed:24911838}; Peripheral membrane protein |
| GO:0005743 mitochondrial inner membrane | IEA GO_REF:0000120 | ACCEPT | Summary: UniProt mapping; consistent. Reason: UniProt SubCell/InterPro mapping (GO_REF:0000120). UniProt curates Coq4 as a peripheral protein of the mitochondrial inner membrane (HAMAP rule MF_03111 plus PMID:16823372/PMID:24911838 evidence tags); the S. pombe GFP data show mitochondrial localisation, while the inner-membrane resolution rests on the curated UniProt location and the conserved COQ synthome biology of the S. cerevisiae ortholog. Supporting Evidence: file:SCHPO/coq4/coq4-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion inner membrane file:SCHPO/coq4/coq4-uniprot.txt Peripheral membrane protein |
| GO:0006744 ubiquinone biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference; ubiquinone biosynthesis step. Reason: IBA from PAINT node PTN000308947 (PTHR12922, GO_REF:0000033). Supported on the target itself: deletion of coq4 abolishes CoQ synthesis in S. pombe (PMID:24911838), and UniProt curates the ubiquinone biosynthesis pathway with experimental evidence from the same study; the IBA additionally indicates the role is inherited across the COQ4 family. Coq4 catalyses the C1 oxidative decarboxylation (PMID:38295803), so it does part of the work. Supporting Evidence: PMID:24911838 the Δcoq4, Δcoq5, Δcoq6, and Δcoq9 strains are also unable to synthesize CoQ file:SCHPO/coq4/coq4-uniprot.txt PATHWAY: Cofactor biosynthesis; ubiquinone biosynthesis. |
| GO:0006744 ubiquinone biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: Mapping; consistent. Reason: UniRule/InterPro/UniPathway mapping (GO_REF:0000120). Same claim as the IMP and IBA rows: the S. pombe coq4 deletion cannot synthesize CoQ (PMID:24911838), and UniProt curates the ubiquinone biosynthesis pathway. Supporting Evidence: PMID:24911838 the Δcoq4, Δcoq5, Δcoq6, and Δcoq9 strains are also unable to synthesize CoQ file:SCHPO/coq4/coq4-uniprot.txt PATHWAY: Cofactor biosynthesis; ubiquinone biosynthesis. |
| GO:0006744 ubiquinone biosynthetic process | IMP PMID:24911838 Functional conservation of coenzyme Q biosynthetic genes amo... | ACCEPT | Summary: Deletion abolishes CoQ10 production (systematic analysis of the S. pombe coq genes). Reason: Deletion of the gene abolishes CoQ10 synthesis and gives the shared coq-mutant phenotypes (PMID:24911838). Coq4 performs a step of the pathway, so it does part of the work; core process. 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. PMID:24911838 Overall, these data indicate that, like the S. pombe Δdps1, Δdlp1, Δppt1/coq2, Δcoq3, Δcoq7, and Δcoq8 strains described previously, the Δcoq4, Δcoq5, Δcoq6, and Δcoq9 strains are also unable to synthesize CoQ. |
| GO:0008270 zinc ion binding | IEA GO_REF:0000104 | KEEP AS NON CORE | Summary: Zinc cofactor of the Coq4-family decarboxylase; subsidiary. Reason: UniRule mapping (GO_REF:0000104). Rests on family membership: the HAMAP Coq4 rule (MF_03111) assigns a Zn(2+) cofactor and four zinc-binding residues (174, 175, 178, 190) to Coq4-family members; no S. pombe metal assay exists. Kept as a non-core cofactor property. Same action as the S. cerevisiae COQ4 review. Supporting Evidence: file:SCHPO/coq4/coq4-uniprot.txt Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000255|HAMAP-Rule:MF_03111}; file:SCHPO/coq4/coq4-uniprot.txt HAMAP; MF_03111; Coq4; 1. |
| GO:0016831 carboxy-lyase activity | IEA GO_REF:0000104 | MODIFY | Summary: Generic carboxy-lyase from UniRule; correct but general for the Coq4 C1 decarboxylase. Reason: UniRule mapping (GO_REF:0000104). Correct but general: the specific activity, GO:0120539 4-hydroxy-3-methoxy-5-polyprenylbenzoate decarboxylase activity, is an is_a descendant that the gene already carries (IBA, IEA, ISS), assigned by HAMAP MF_03111 and supported for the COQ4 family by PMID:38295803. MODIFY to that term, as in the S. cerevisiae COQ4 review. Proposed replacements: 4-hydroxy-3-methoxy-5-polyprenylbenzoate decarboxylase activity Supporting Evidence: file:SCHPO/coq4/coq4-uniprot.txt Lyase that catalyzes the C1-decarboxylation of 4-hydroxy-3-methoxy-5-(all-trans-decaprenyl)benzoic acid into 2-methoxy-6-(all-trans-decaprenyl)phenol during ubiquinone biosynthesis. PMID:38295803 Here, we provide evidence that these two reactions occur in a single oxidative decarboxylation step catalyzed by COQ4. |
| GO:0031314 extrinsic component of mitochondrial inner membrane | IC GO_REF:0000111 | ACCEPT | Summary: Peripheral component on the matrix side of the inner membrane, where the CoQ synthome assembles. Reason: Curator inference (IC, GO_REF:0000111). UniProt curates Coq4 as a peripheral membrane protein on the matrix side of the mitochondrial inner membrane (HAMAP rule MF_03111 with PMID:16823372 cited); the peripheral/matrix-side resolution rests on that curated location and on the COQ4 family biology rather than on a fractionation assay in S. pombe. The S. cerevisiae ortholog carries IDA support for this term (COQ4 review). Accepted. Supporting Evidence: file:SCHPO/coq4/coq4-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion inner membrane file:SCHPO/coq4/coq4-uniprot.txt Peripheral membrane protein |
| GO:0031314 extrinsic component of mitochondrial inner membrane | IEA GO_REF:0000104 | ACCEPT | Summary: Peripheral component on the matrix side of the inner membrane, where the CoQ synthome assembles. Reason: UniRule mapping (GO_REF:0000104). UniProt curates Coq4 as a peripheral membrane protein on the matrix side of the mitochondrial inner membrane (HAMAP rule MF_03111 with PMID:16823372 cited); the peripheral/matrix-side resolution rests on that curated location and on the COQ4 family biology rather than on a fractionation assay in S. pombe. The S. cerevisiae ortholog carries IDA support for this term (COQ4 review). Accepted. Supporting Evidence: file:SCHPO/coq4/coq4-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion inner membrane file:SCHPO/coq4/coq4-uniprot.txt Peripheral membrane protein |
| GO:0120539 4-hydroxy-3-methoxy-5-polyprenylbenzoate decarboxylase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Coq4 is the CoQ ring decarboxylase (PAINT/EC/similarity), matching the S. cerevisiae COQ4 review. Reason: IBA from PAINT node PTN000308947 (PTHR12922, GO_REF:0000033). The C1 decarboxylase activity rests on COQ4-family membership (HAMAP MF_03111) and on the demonstration that COQ4 catalyses the C1 oxidative decarboxylation in heterologous hosts (PMID:38295803); there is no S. pombe Coq4 enzyme assay, but the S. pombe deletion cannot make CoQ (PMID:24911838) and human COQ4 complements it. Core function, matching the S. cerevisiae and human COQ4 reviews and the module annoton. Supporting Evidence: file:SCHPO/coq4/coq4-uniprot.txt Lyase that catalyzes the C1-decarboxylation of 4-hydroxy-3-methoxy-5-(all-trans-decaprenyl)benzoic acid into 2-methoxy-6-(all-trans-decaprenyl)phenol during ubiquinone biosynthesis. file:SCHPO/coq4/coq4-uniprot.txt Reaction=4-hydroxy-3-methoxy-5-(all-trans-decaprenyl)benzoate + H(+) = 2-methoxy-6-(all-trans-decaprenyl)phenol + CO2 PMID:38295803 Here, we provide evidence that these two reactions occur in a single oxidative decarboxylation step catalyzed by COQ4. PMID:24911838 Similar results were obtained when HsCOQ4 and HsCOQ6 were expressed in the Δcoq4 and Δcoq6 strains, respectively (Figures 6A and 6B). |
| GO:0120539 4-hydroxy-3-methoxy-5-polyprenylbenzoate decarboxylase activity | IEA GO_REF:0000003 | ACCEPT | Summary: Coq4 is the CoQ ring decarboxylase (PAINT/EC/similarity), matching the S. cerevisiae COQ4 review. Reason: EC mapping (GO_REF:0000003). The C1 decarboxylase activity rests on COQ4-family membership (HAMAP MF_03111) and on the demonstration that COQ4 catalyses the C1 oxidative decarboxylation in heterologous hosts (PMID:38295803); there is no S. pombe Coq4 enzyme assay, but the S. pombe deletion cannot make CoQ (PMID:24911838) and human COQ4 complements it. Core function, matching the S. cerevisiae and human COQ4 reviews and the module annoton. Supporting Evidence: file:SCHPO/coq4/coq4-uniprot.txt Lyase that catalyzes the C1-decarboxylation of 4-hydroxy-3-methoxy-5-(all-trans-decaprenyl)benzoic acid into 2-methoxy-6-(all-trans-decaprenyl)phenol during ubiquinone biosynthesis. file:SCHPO/coq4/coq4-uniprot.txt Reaction=4-hydroxy-3-methoxy-5-(all-trans-decaprenyl)benzoate + H(+) = 2-methoxy-6-(all-trans-decaprenyl)phenol + CO2 PMID:38295803 Here, we provide evidence that these two reactions occur in a single oxidative decarboxylation step catalyzed by COQ4. PMID:24911838 Similar results were obtained when HsCOQ4 and HsCOQ6 were expressed in the Δcoq4 and Δcoq6 strains, respectively (Figures 6A and 6B). |
| GO:0120539 4-hydroxy-3-methoxy-5-polyprenylbenzoate decarboxylase activity | ISS GO_REF:0000024 | ACCEPT | Summary: Coq4 is the CoQ ring decarboxylase (PAINT/EC/similarity), matching the S. cerevisiae COQ4 review. Reason: PomBase ISS from human COQ4 (GO_REF:0000024). The C1 decarboxylase activity rests on COQ4-family membership (HAMAP MF_03111) and on the demonstration that COQ4 catalyses the C1 oxidative decarboxylation in heterologous hosts (PMID:38295803); there is no S. pombe Coq4 enzyme assay, but the S. pombe deletion cannot make CoQ (PMID:24911838) and human COQ4 complements it. Core function, matching the S. cerevisiae and human COQ4 reviews and the module annoton. Supporting Evidence: file:SCHPO/coq4/coq4-uniprot.txt Lyase that catalyzes the C1-decarboxylation of 4-hydroxy-3-methoxy-5-(all-trans-decaprenyl)benzoic acid into 2-methoxy-6-(all-trans-decaprenyl)phenol during ubiquinone biosynthesis. file:SCHPO/coq4/coq4-uniprot.txt Reaction=4-hydroxy-3-methoxy-5-(all-trans-decaprenyl)benzoate + H(+) = 2-methoxy-6-(all-trans-decaprenyl)phenol + CO2 PMID:38295803 Here, we provide evidence that these two reactions occur in a single oxidative decarboxylation step catalyzed by COQ4. PMID:24911838 Similar results were obtained when HsCOQ4 and HsCOQ6 were expressed in the Δcoq4 and Δcoq6 strains, respectively (Figures 6A and 6B). |
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