Sulfide Oxidation Children — Obsoletion & Replacement

IN_PROGRESS OBSOLETION

Sulfide Oxidation Children — Obsoletion & Replacement

Overview

A GO obsoletion has retired three molecular-mechanism-specific
children of GO:0019418 sulfide oxidation, because they were more
specific than any known gene product and 2 of the 3 had no
annotations. All affected annotations should be migrated to the
parent term GO:0019418 (with the appropriate substrate/specificity
captured in evidence rather than the term ID).

Replaced by:

The textual definition of GO:0019418 was simultaneously updated to
"The chemical reactions and pathways resulting in the conversion of
sulfide to sulfite or sulfate." The MetaCyc cross-references on the
obsoleted children were redirected to GO:0019418
(MetaCyc:P222-PWY, MetaCyc:PWY-5274, MetaCyc:PWY-5285,
MetaCyc:PWY-7927).

Upstream tickets

Obsoletion plan (per upstream)

Obsoleted term ID Replacement
sulfide oxidation, using sulfide:quinone oxidoreductase GO:0070221 (obsolete) GO:0019418 sulfide oxidation
sulfide oxidation, using sulfide dehydrogenase GO:0070222 (obsolete) GO:0019418 sulfide oxidation
sulfide oxidation, using sulfur dioxygenase GO:0070223 (obsolete) GO:0019418 sulfide oxidation

Affected experimental / direct annotations (GO:0070221 only)

GO:0070222 and GO:0070223 had zero direct annotations at
obsoletion time. All affected annotations are on GO:0070221.

Group Gene Species UniProt Evidence Reference / Source Status
UniProt SQOR Homo sapiens (NCBITaxon:9606) Q9Y6N5 IDA (ECO:0000314) UniProtKB pending move to GO:0019418
UniProt TSTD1 Homo sapiens (NCBITaxon:9606) Q8NFU3 TAS (ECO:0000304) UniProtKB pending move to GO:0019418
UniProt SLC25A10 Homo sapiens (NCBITaxon:9606) Q9UBX3 TAS (ECO:0000304) UniProtKB pending move to GO:0019418
RGD Sqor Rattus norvegicus (NCBITaxon:10116) — ISO (ECO:0000266) RGD pending move
MGI Sqor Mus musculus (NCBITaxon:10090) — ISS/ISO (ECO:0000250, ECO:0000266) MGI pending move

A larger pool of IBA (ECO:0000318) annotations propagated from
PANTHER will be remapped to GO:0019418 automatically once the next
PAINT/IBA pipeline run picks up the obsoletion. These span SQOR
orthologs across vertebrates (Bos taurus, Gallus gallus, Xenopus
tropicalis, Danio rerio, Anolis carolinensis, gorilla, chimp, etc.),
fungal/protist orthologs (Paramecium tetraurelia, Aspergillus
nidulans, Neurospora crassa, Cryptococcus deneoformans, S. pombe
hmt2, S. japonicus hmt2, Dictyostelium purpureum), bacterial homologs
(Pseudomonas aeruginosa PA2345, Staphylococcus aureus, Chloroflexus
aurantiacus), and a Monosiga brevicollis SQOR. These are
auto-migrated and do not need per-annotation work here.

InterPro2GO / mapping cleanup (per upstream issue)

Impact on this repo

No genes annotated to GO:0070221/222/223 are currently reviewed in
this repo:

So no existing reviews need refresh for the obsoletion itself.
The opportunity here is that SQOR is otherwise unreviewed in
this repo despite being a well-characterized human mitochondrial
sulfide-oxidizing enzyme directly relevant to H2S signaling, sulfide
detoxification, and the inherited mitochondrial disorder caused by
SQOR deficiency (PMID:31108281; affects 1 of the 3 known annotations
queued for migration).

Scope

Candidate genes for initial review

Verify each with just fetch-gene <organism> <gene> before starting
and confirm UniProt accessions. None are currently in the repo.

Tier 1 — direct experimental annotation, well-characterized

  1. SQOR / Q9Y6N5 (Homo sapiens) — mitochondrial sulfide:quinone
    oxidoreductase, the canonical human enzyme for sulfide oxidation
    in the first step of mitochondrial H2S detoxification. The IDA
    annotation on GO:0070221 is the 1 EXP that the upstream issue
    flags for migration. SQOR also carries an IBA on GO:0070221. A
    review here should anchor the BP on GO:0019418 (post-obsoletion)
    and confirm the MF anchor remains GO:0047804 sulfide:quinone
    reductase activity. Clinically relevant (SQOR deficiency causes
    Leigh-like mitochondrial encephalopathy).

Tier 2 — TAS, less direct

  1. TSTD1 / Q8NFU3 (Homo sapiens) — thiosulfate sulfurtransferase-
    like domain-containing 1; carries a TAS annotation on GO:0070221
    plus an IEA. Its primary characterized activity is rhodanese-type
    thiosulfate:glutathione sulfurtransferase (PMID:24107290), and
    InterPro has already removed the IPR042457 → GO:0070221 mapping
    per the upstream issue. A review would assess whether GO:0019418
    (the obsoletion replacement) or a different sulfurtransferase BP
    is the right placement.
  2. SLC25A10 / Q9UBX3 (Homo sapiens) — mitochondrial
    dicarboxylate carrier; TAS on GO:0070221. The annotation is on a
    pathway role rather than direct enzymatic activity; review would
    determine whether GO:0019418 is appropriate or whether this
    annotation should be retracted in favor of transport-centric BPs.

Tier 3 — opportunistic, non-human

  1. hmt2 / SPBC2G5.06c (Schizosaccharomyces pombe) — fission yeast
    ortholog carrying an IBA on GO:0070221. Would extend SCHPO
    coverage but lower priority since IBA migration is automatic.

Proposed approach

  1. Obsoletion has landed. All three terms are obsolete in the
    ontology and the upstream ontology ticket is closed. The
    annotation-migration work in go-annotation#6388 is the only
    remaining loose end upstream (still open as of 2026-05-15, with
    the InterPro mapping removed the same day).
  2. Start with human SQOR. Run just fetch-gene human SQOR and
    confirm the GOA pull picks up the obsoletion: GO:0070221 should
    appear as an obsolete term (or already have been remapped to
    GO:0019418). Review per CLAUDE.md, paying attention to:
  3. The cognate MF GO:0047804 sulfide:quinone reductase activity
    (intact) is the right MF anchor.
  4. The BP anchor should be GO:0019418 sulfide oxidation
    (post-obsoletion).
  5. SQOR also participates in CoQ/electron-transport context;
    check that any CC/BP claims about mitochondrial ETC
    integration are evidence-backed.
  6. Follow with TSTD1 then SLC25A10. Both are TAS-only on the
    obsoleted term and the upstream mapping (IPR042457 → GO:0070221)
    has already been removed; review should evaluate whether
    GO:0019418 is even the right BP or whether the original TAS was
    on shaky ground.
  7. Defer S. pombe hmt2 and the bacterial homologs unless they
    come up via other workstreams; the IBA propagations will be
    auto-migrated.
  8. Do not create reviews for the IBA-only orthologs listed in
    the impact table — they will be remapped automatically.

Priority

Medium-low. Only 3 direct (non-IBA) annotations are affected
and the ontology change is already in production. The migration
upstream is small. However, human SQOR is a clinically and
biologically important gene with no review yet in this repo, so
this obsoletion is a reasonable trigger to add it. The other two
human entries (TSTD1, SLC25A10) are TAS-only and lower value.

Status