SPBC3H7.04 (mS42; also referred to as bot1 in early functional studies) is a 220 aa mitochondrion-specific small ribosomal subunit protein of the fission yeast Schizosaccharomyces pombe. It is a structural component of the 37S mitochondrial small ribosomal subunit (mt-SSU), forming a dimer with mS43 that builds a large protuberance adjacent to the mRNA channel exit; the S. cerevisiae ortholog (Rsm26p / mS42; MrpS35p family) is visualized in this location in cryo-EM structures of the yeast mitoribosome. Its role is thus one of the many mitochondrion-specific ribosomal proteins that are required for mitochondrial translation of the respiratory-chain subunits encoded on mtDNA. Although the protein carries an Iron/manganese superoxide dismutase C-terminal fold (IPR019832 / Pfam PF02777 / SUPFAM SSF54719 / Gene3D 3.55.40.20), this is fold-only ancestry (the mitochondrial ribosome inherited the mS42/mS43 protein pair from the bacterial ancestor of mitochondria) and the protein is not a superoxide dismutase — no PROSITE Mn/Fe-SOD active-site signature matches, no metal-coordinating catalytic residues have been demonstrated, and the PANTHER subfamily assignment (PTHR43595:SF2) is the mitoribosomal branch, not the SOD branch. bot1 is essential for viability and its depletion causes defective mitochondrial protein synthesis, loss of mitochondrial network integrity, reduced respiration, and altered cell morphology (Wiley et al. 2008, PMID:18245278).
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | REMOVE | Summary: IBA "cytoplasm" propagated from PANTHER family PTHR43595 (Iron/Manganese Superoxide Dismutase). The WITH/FROM list is dominated by canonical Fe/Mn-SOD paralogs (e.g. SGD:S000002755 = SOD2, UniProtKB:P00448 = SodA), which are legitimately cytoplasmic / mitochondrial-matrix SODs. The mS42/mS43 mitoribosomal branch of PTHR43595 is a separate subfamily (PTHR43595:SF2 = SMALL RIBOSOMAL SUBUNIT PROTEIN MS42) whose members reside in the mitochondrial small ribosomal subunit — mitochondrion is not a child of cytoplasm in the GO CC hierarchy, so `cytoplasm` is not just non-specific but sub-cellularly wrong for this protein. The correct specific location is already independently supported by NAS/ISO/IEA annotations to mitochondrion / mitochondrial small ribosomal subunit. Reason: IBA over-propagation from the SOD side of a family that also contains the mitoribosomal mS42 subfamily; the correct sub-cellular location (mitochondrial small ribosomal subunit) is already captured by NAS (PMID:18245278) and ISO (from SGD:S000003862) annotations, so no information is lost. Propagation Review Root cause: PROPAGATION BAD Failure modes: WRONG ORTHOLOG OR PARALOG COMPARTMENT OR COMPLEX MISMATCH Supporting Evidence: UniProt:O74379 SUBCELLULAR LOCATION: Mitochondrion UniProt:O74379 SIMILARITY: Belongs to the mitochondrion-specific ribosomal protein mS42 family. |
| GO:0004784 superoxide dismutase activity | IEA GO_REF:0000002 | REMOVE | Summary: InterPro2GO annotation from IPR019832 (Iron/manganese superoxide dismutase, C-terminal domain). IPR019832 is a fold/superfamily entry — matching it means the protein has the Fe/Mn-SOD C-terminal *fold*, not necessarily the catalytic activity. SPBC3H7.04 is the mS42 mitoribosomal small-subunit protein: it retains the SOD fold by ancestry (mitochondria are of bacterial origin, and the mitoribosome inherited multiple protein pairs that co-opted enzyme folds as purely structural components), but it does not match any PROSITE Mn/Fe-SOD active-site pattern, has no biochemical evidence of dismutase activity, and is classified by PANTHER's subfamily model (PTHR43595:SF2) as a mitoribosomal protein, not a SOD. Val Wood's upstream flag (geneontology/go-annotation#6474) explicitly diagnoses this as a fold-reuse pseudo-SOD — the same annotation-error class as the Cu/Zn-SOD pseudoenzymes documented in `projects/PSEUDOENZYMES.md`. Reason: Fold-only InterPro2GO match; the protein is a mitoribosomal structural component, not a superoxide dismutase. Removing the SOD MF also removes the incorrect logical-inference chain that generated GO:0019430 (removal of superoxide radicals). This is the exact class of over-annotation the INTERPRO project targets. Supporting Evidence: file:SCHPO/SPBC3H7.04/SPBC3H7.04-uniprot.txt FUNCTION: Component of the mitochondrial ribosome (mitoribosome) UniProt:O74379 SIMILARITY: Belongs to the mitochondrion-specific ribosomal protein mS42 family. file:SCHPO/SPBC3H7.04/SPBC3H7.04-notes.md structurally classified in the SOD superfamily |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Electronic annotation mapped from the UniProt "SUBCELLULAR LOCATION: Mitochondrion" statement (Swiss-Prot SL-0173). The mitochondrial localization is supported by the by-similarity call to the yeast ortholog (UniProtKB:P10662) and by ComplexPortal membership in the 37S mt-SSU (CPX-10315). Cellular-component annotation should ideally be at the more specific `GO:0005763 mitochondrial small ribosomal subunit` child (already present via ISO and NAS), but this parent term is not wrong. Reason: Correct but generic location; the specific `mitochondrial small ribosomal subunit` term (already present via ISO/NAS) is the core location. Supporting Evidence: UniProt:O74379 SUBCELLULAR LOCATION: Mitochondrion |
| GO:0006801 superoxide metabolic process | IEA GO_REF:0000002 | REMOVE | Summary: InterPro2GO annotation from IPR019832 (Fe/Mn SOD C-terminal domain fold). Same fold-match rationale as the MF SOD-activity annotation: the protein does not perform superoxide-related chemistry — it is a structural component of the mt-SSU. The BP term is a direct downstream consequence of assuming SOD activity and is not supported by any independent evidence for this gene. Reason: Downstream over-annotation of the pseudo-SOD IEA chain; no independent biological evidence links mS42 to superoxide metabolism. Supporting Evidence: file:SCHPO/SPBC3H7.04/SPBC3H7.04-uniprot.txt FUNCTION: Component of the mitochondrial ribosome (mitoribosome) file:SCHPO/SPBC3H7.04/SPBC3H7.04-notes.md `IEA with IPR019832 → GO:0004784 superoxide dismutase activity` |
| GO:0019430 removal of superoxide radicals | IEA GO_REF:0000108 | REMOVE | Summary: Automated inter-ontology inference (GO_REF:0000108) from GO:0004784 (SOD activity). Because the parent MF annotation is a fold-only over-annotation (see above), the derived BP annotation inherits the same defect: mS42 does not remove superoxide radicals — it is a structural mitoribosomal protein. Removing the parent MF resolves this without any biological information loss. Reason: Logical-inference product of the incorrect SOD-activity IEA; falls away when the MF is removed. Supporting Evidence: file:SCHPO/SPBC3H7.04/SPBC3H7.04-uniprot.txt FUNCTION: Component of the mitochondrial ribosome (mitoribosome) |
| GO:0046872 metal ion binding | IEA GO_REF:0000002 | REMOVE | Summary: InterPro2GO annotation from IPR019832 (Fe/Mn SOD C-terminal domain fold). The metal-ion-binding MF term is only appropriate for members of the family that coordinate an Mn or Fe catalytic ion; the mS42 mitoribosomal subfamily has no evidence of metal coordination and no PROSITE Mn/Fe-SOD active-site match. There is no independent evidence that mS42 binds a catalytically relevant metal ion in vivo. Reason: Fold-only over-annotation; no evidence of metal binding in the mitoribosomal mS42 subfamily. Supporting Evidence: file:SCHPO/SPBC3H7.04/SPBC3H7.04-uniprot.txt FUNCTION: Component of the mitochondrial ribosome (mitoribosome) file:SCHPO/SPBC3H7.04/SPBC3H7.04-notes.md the metal-coordinating catalytic residues |
| GO:0005763 mitochondrial small ribosomal subunit | NAS PMID:18245278 Bot1p is required for mitochondrial translation, respiratory... | ACCEPT | Summary: ComplexPortal-assigned NAS annotation citing Wiley et al. 2008: the paper shows the S. pombe protein Bot1p (identified as the S. pombe counterpart of the S. cerevisiae MrpS35p / Rsm26p family) localizes to mitochondria and cofractionates with purified mitochondrial ribosomes. ComplexPortal has SPBC3H7.04 as a component of the 37S mt-SSU (CPX-10315). This is the correct, core cellular-component annotation for the gene. Reason: Directly supported by primary literature (cofractionation with mitoribosomes) and by ComplexPortal complex membership; the correct core CC annotation. Supporting Evidence: PMID:18245278 Bot1p localizes to the mitochondria in live cells and cofractionates with purified mitochondrial ribosomes. UniProt:O74379 SUBUNIT: Component of the mitochondrial small ribosomal subunit (mt-SSU). |
| GO:0032543 mitochondrial translation | NAS PMID:18245278 Bot1p is required for mitochondrial translation, respiratory... | ACCEPT | Summary: ComplexPortal-assigned NAS annotation citing Wiley et al. 2008: bot1 is required for mitochondrial protein synthesis, and its depletion causes decreased mitochondrial translation with a corresponding drop in cell respiration. Core biological-process annotation for a mitoribosomal structural subunit. Reason: Directly supported by primary literature (loss-of-function phenotype is decreased mitochondrial protein translation); the correct core BP annotation. Supporting Evidence: PMID:18245278 Reduced levels of Bot1p lead to mitochondrial fragmentation, decreased mitochondrial protein translation, and a corresponding decrease in cell respiration. |
| GO:0005739 mitochondrion | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: ISS annotation from the S. cerevisiae ortholog UniProtKB:P10662, redundant with the UniProt SubCell-derived IEA above. Correct location call; already captured at the more specific `mt-SSU` child. Reason: Correct but redundant with the more specific mt-SSU annotations; the core location is `GO:0005763 mitochondrial small ribosomal subunit`. Supporting Evidence: UniProt:O74379 SUBCELLULAR LOCATION: Mitochondrion |
| GO:0003735 structural constituent of ribosome | ISO GO_REF:0000024 | ACCEPT | Summary: ISO annotation transferred by PomBase from the S. cerevisiae ortholog SGD:S000003862 (Rsm26p / mS42). This is the correct core molecular function for a mitoribosomal structural subunit — the protein's contribution to the mitoribosome is structural (part of the mS42/mS43 protuberance adjacent to the mRNA channel exit), not catalytic. This annotation should stand in place of the incorrect SOD-activity IEA. Reason: Correct core MF; supported by the ortholog's characterization and by the mS42-mS43 dimer's structural role in the mt-SSU. Supporting Evidence: UniProt:O74379 mS43 forms a dimer with mS42, building a large protuberance adjacent to the mRNA channel exit in the mt-SSU body. |
| GO:0005763 mitochondrial small ribosomal subunit | ISO GO_REF:0000024 | ACCEPT | Summary: ISO annotation from S. cerevisiae SGD:S000003862 (Rsm26p) — independent orthology-based support for the same conclusion as the NAS annotation above. Reason: Correct core CC; corroborates the NAS annotation and matches the UniProt/ComplexPortal-curated complex membership. Supporting Evidence: UniProt:O74379 SUBUNIT: Component of the mitochondrial small ribosomal subunit (mt-SSU). |
| GO:0032543 mitochondrial translation | ISO GO_REF:0000024 | ACCEPT | Summary: ISO annotation from S. cerevisiae SGD:S000003862 (Rsm26p) — independent orthology-based support for the same conclusion as the NAS annotation above. Reason: Correct core BP; corroborates the NAS annotation and is consistent with the loss-of-function phenotype reported in PMID:18245278. Supporting Evidence: PMID:18245278 Reduced levels of Bot1p lead to mitochondrial fragmentation, decreased mitochondrial protein translation, and a corresponding decrease in cell respiration. |
Loading supporting content…
Download this section (compressed HTML)Q: Does S. pombe mS42 (SPBC3H7.04) retain any residual metal-binding or superoxide-related activity, or is the SOD-fold reuse purely structural? A cryo-EM structure of the S. pombe mt-SSU (or a targeted structural prediction) at the mS42 position, together with an in-vitro superoxide-dismutase assay on the recombinant protein, would resolve whether the annotation should be `REMOVE` (as done here) or `MODIFY` to a residual/regulatory metal-binding term.
Q: How many other members of the IPR019832 InterPro entry are mitoribosomal mS42-family proteins rather than SODs? A cross-taxonomic scan of PTHR43595:SF2 subfamily members would let InterPro consider adding a subfamily-level `NOT` annotation for the SOD MF/BP terms, or down-scoping the InterPro2GO mapping.
Experiment: Recombinant expression of SPBC3H7.04 in E. coli followed by a standard xanthine/xanthine-oxidase or pyrogallol autoxidation SOD activity assay, with human SOD2 and E. coli SodA as positive controls. A negative result would give direct biochemical confirmation of the pseudoenzyme classification and support the `REMOVE` action for the SOD-activity IEA.
Experiment: Ribosome-profiling / polysome-fractionation of a conditional depletion of SPBC3H7.04 (extending Wiley et al. 2008 to sub-cellular resolution) to quantify the specific mitochondrial-translation defect at the level of individual mtDNA-encoded transcripts. This would strengthen the mitochondrial-translation involvement annotation beyond NAS/ISO evidence.
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)