J7SF87 is the 422-residue Y9C9A.16b product of the Caenorhabditis elegans gene sqrd-2 (WBGene00021183), one of two worm paralogs of the mitochondrial sulfide:quinone oxidoreductase (SQOR) of animals; the other is sqrd-1, with which it shares about 75% identity. It belongs to the FAD-dependent SQRD family and keeps the N-terminal GxGxxG FAD-binding motif and both catalytic cysteines that form the persulfide intermediate in human SQOR. By orthology it is expected to oxidize hydrogen sulfide, transfer the sulfane sulfur to glutathione and pass the electrons to the mitochondrial quinone pool; docking models accommodate both ubiquinone and rhodoquinone. The gene, once classed as a pseudogene, is expressed, but unlike sqrd-1 it is not induced by H2S. A deletion mutant is not sensitive to H2S and recovers from sulfide exposure slightly faster than wild type, so its physiological role is unresolved. Expression rises strongly in mutants of the NCoR/SMRT homologue gei-8. The shorter Y9C9A.16a product lacks the FAD motif. No enzyme assay or localization study of the worm protein has been reported.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: Mitochondrion (is_active_in) propagated by PAINT from the SQR node seeded by fission yeast Hmt2 and human SQOR. Reason: Under the root-organelle policy the organelle claim was checked. J7SF87 sits in the mitochondrial SQR subfamily (PANTHER PTHR10632:SF2) whose experimentally characterised members, human SQOR and S. pombe Hmt2, are mitochondrial, and the catalytic cycle reduces the mitochondrial quinone pool (ubiquinone or rhodoquinone). J7SF87 is inside that clade and retains the catalytic and FAD-binding residues, so there is no sign of divergence that would argue against the node placement. One caveat: the J7SF87 model has no counterpart of the human N-terminal transit peptide, so targeting rests on family membership and function rather than a detectable presequence; the same holds for SQRD-1. No sub-compartment is added because only the homology line supports the inner membrane. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000066987 SUPPORTS TRANSFER Mitochondrial SQR node; J7SF87 descends within it and shows no sign of divergence. UniProtKB:Q9Y6N5 · human SQOR SUPPORTS TRANSFER PomBase:SPBC2G5.06c · hmt2 SUPPORTS TRANSFER Supporting Evidence: file:worm/J7SF87/J7SF87-uniprot.txt PTHR10632:SF2; SULFIDE:QUINONE OXIDOREDUCTASE, MITOCHONDRIAL file:worm/J7SF87/J7SF87-bioinformatics/RESULTS.md J7SF87 begins 17 residues before that motif, so it has no counterpart of the N-terminal extension (mitochondrial transit peptide) of human SQOR. |
| GO:0005739 mitochondrion | IEA GO_REF:0000120 | ACCEPT | Summary: Mitochondrion from the UniProt subcellular-location ARBA rule. Reason: The ARBA rule is not evidence on its own, but the organelle claim holds for the reasons given for the IBA row: membership of the mitochondrial SQR subfamily and a catalytic cycle that feeds the mitochondrial quinone pool. Consistent with the IBA row; no direct localization of the worm protein exists. Supporting Evidence: file:worm/J7SF87/J7SF87-deep-research-manual.md No enzyme assay, purified protein, localization study or structure of worm SQRD-2. file:worm/J7SF87/J7SF87-uniprot.txt PTHR10632:SF2; SULFIDE:QUINONE OXIDOREDUCTASE, MITOCHONDRIAL PMID:39178951 UQ and RQ were kept in the quinone site of SQRD-1 and SQRD-2 and within a distance compatible with an electron transfer reaction during the simulation. |
| GO:0070224 sulfide:quinone oxidoreductase activity | IBA GO_REF:0000033 | MODIFY | Summary: Sulfide:quinone oxidoreductase activity propagated by PAINT from the SQR node seeded by human SQOR and fission yeast Hmt2. Reason: The enzyme class is right and the propagation is sound: J7SF87 is 45% identical to human SQOR and keeps both catalytic persulfide cysteines (human Cys201 and Cys379, J7SF87 Cys169 and Cys351) and the FAD-binding motif. But GO:0070224 is defined by the bacterial-type reaction that releases free sulfane sulfur (S0). The animal mitochondrial SQRs transfer the sulfane sulfur to glutathione, forming S-sulfanylglutathione (EC 1.8.5.8), which is GO:0106436, a sibling of GO:0070224 under GO:0016672 (checked in OLS), not a descendant. The gene already carries GO:0106436 (IEA from EC). The worm acceptor has not been measured, so the refinement rests on orthology, as in the sqrd-1 review. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000066985 SUPPORTS TRANSFER The activity transfers; the node term is the S0-releasing reaction, while the animal members use glutathione as sulfane acceptor (GO:0106436). UniProtKB:Q9Y6N5 · human SQOR SUPPORTS TRANSFER PomBase:SPBC2G5.06c · hmt2 SUPPORTS TRANSFER Proposed replacements: glutathione-dependent sulfide quinone oxidoreductase activity Supporting Evidence: file:worm/J7SF87/J7SF87-bioinformatics/RESULTS.md Both catalytic cysteines of human SQOR (Cys201 and Cys379, the cysteine persulfide intermediates, experimentally defined in Q9Y6N5) are conserved in J7SF87, as Cys169 and Cys351. PMID:21840852 The C. elegans gene sqrd-1 encodes a member of the group II SQRD enzymes, which also includes human, mouse, and Drosophila homologs. |
| GO:0070224 sulfide:quinone oxidoreductase activity | IEA GO_REF:0000117 | MODIFY | Summary: Sulfide:quinone oxidoreductase activity from an ARBA rule. Reason: Same claim as the IBA row and handled the same way: correct enzyme class, but the animal type II SQRs use glutathione as sulfane-sulfur acceptor, which is GO:0106436 (a sibling of GO:0070224, not a descendant), already carried by the gene. Proposed replacements: glutathione-dependent sulfide quinone oxidoreductase activity Supporting Evidence: file:worm/J7SF87/J7SF87-bioinformatics/RESULTS.md J7SF87 retains the catalytic and FAD-binding residues of a functional type II (animal) SQR, so there is no sequence argument for a pseudoenzyme. PMID:21840852 The C. elegans gene sqrd-1 encodes a member of the group II SQRD enzymes, which also includes human, mouse, and Drosophila homologs. |
| GO:0071949 FAD binding | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: FAD binding propagated by PAINT from the SQR node. Reason: FAD is the prosthetic group of SQRs, and J7SF87 keeps the N-terminal GxGxxG dinucleotide-binding motif and the residues aligned to the human SQOR FAD-binding sites. The term is as precise as it can be, but cofactor binding is a part of the catalytic activity rather than a separate core function. Note that the shorter Y9C9A.16a product (Q9N2S1) lacks this motif. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: PANTHER:PTN000066985 SUPPORTS TRANSFER FAD-binding motif and binding-site residues retained in J7SF87. Supporting Evidence: file:worm/J7SF87/J7SF87-bioinformatics/RESULTS.md All human FAD-binding feature positions align to identical or conservative residues in J7SF87 file:worm/J7SF87/J7SF87-uniprot.txt IPR036188; FAD/NAD-bd_sf. |
| GO:0106436 glutathione-dependent sulfide quinone oxidoreductase activity | IEA GO_REF:0000003 | ACCEPT | Summary: Glutathione-dependent SQR activity from the EC 1.8.5.8 mapping. Reason: This is the expected activity of an animal mitochondrial SQR. J7SF87 conserves both catalytic persulfide cysteines and the FAD-binding residues of human SQOR, and its quinone site is modelled to bind ubiquinone and rhodoquinone. The activity is inferred by homology: no assay of worm SQRD-2 exists, its glutathione use is not measured, and the deletion mutant is not H2S-sensitive, so how much it contributes to sulfide oxidation in vivo is open. Supporting Evidence: file:worm/J7SF87/J7SF87-bioinformatics/RESULTS.md Both catalytic cysteines of human SQOR (Cys201 and Cys379, the cysteine persulfide intermediates, experimentally defined in Q9Y6N5) are conserved in J7SF87, as Cys169 and Cys351. PMID:39178951 Both quinones bind similarly to C. elegans SQRD-1 and SQRD-2. PMID:23484030 encodes a sulfide:quinone oxidoreductase that we name sqrd-2 |
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Download this section (compressed HTML)Q: Is SQRD-2 catalytically active as a sulfide:quinone oxidoreductase, and with which sulfane acceptor (glutathione, sulfite) and quinone (ubiquinone, rhodoquinone)? Should it carry sulfide oxidation (GO:0019418), as SQRD-1 does, once activity is shown? UniProt still lists the obsoleted IBA GO:0070221 for this entry.
Q: Why does sqrd-2 loss speed recovery from sulfide rather than slow it? Does SQRD-2 compete with SQRD-1 for quinone or acceptor, or act in a different tissue or developmental stage?
Q: How is SQRD-2 targeted to mitochondria without a recognizable N-terminal presequence, and is the FAD-motif-less Y9C9A.16a product (Q9N2S1) expressed and functional?
Experiment: Express recombinant SQRD-2 (Y9C9A.16b) and measure sulfide-dependent reduction of decylubiquinone and rhodoquinone analogues with glutathione, sulfite or cyanide as acceptor, alongside SQRD-1; mutate Cys169 and Cys351 as controls.
Hypothesis: SQRD-2 is an active glutathione-dependent SQR with the catalytic cysteines of human SQOR.
Experiment: Co-localize endogenously tagged SQRD-2 (CRISPR knock-in) with a mitochondrial marker, and test sqrd-1; sqrd-2 double mutants for H2S sensitivity and sulfide consumption.
Hypothesis: SQRD-2 is mitochondrial and contributes to sulfide oxidation redundantly with SQRD-1.
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