Oxidative Phosphorylation (OXPHOS) Project

Overview

Oxidative phosphorylation is the metabolic pathway by which mitochondria generate ATP through
electron transport and chemiosmotic coupling. The electron transport chain (ETC) comprises four
multi-subunit complexes (I-IV) embedded in the mitochondrial inner membrane, plus two mobile
electron carriers (ubiquinone/CoQ10 and cytochrome c). Complex V (ATP synthase) uses the
resulting proton gradient to synthesize ATP.

OXPHOS is responsible for ~90% of cellular ATP production and is unique in requiring
coordinated expression from both nuclear and mitochondrial genomes: 13 subunits are
mtDNA-encoded, while ~80 structural subunits and dozens of assembly factors are nuclear-encoded.

Fig. 3 from Martínez-Reyes & Chandel (2020) PMID:31911585.
The TCA cycle and OXPHOS are tightly coordinated. Complex II (SDH) uniquely bridges both
pathways: the succinate → fumarate reaction (TCA step 6) simultaneously feeds electrons
into the ETC via FAD → FADH₂ → Fe-S → ubiquinone.

Generic OXPHOS module

This project began as a gene-by-gene annotation review (below), which predates
the Module KB. A taxon-neutral, recursively decomposable module for the whole
pathway now lives at modules/oxphos.yaml. It models
OXPHOS as a coupled ETC + ATP-synthesis process, represents each respiratory
complex as a PROTEIN_COMPLEX node carrying its complex-level catalytic
activity (subunits as active_units, not separate annotons), recursively
decomposes the modular complexes (Complex I N/Q/P arms; ATP synthase F1/Fo), and
captures lineage variants (type-II NADH dehydrogenase, alternative oxidase,
bacterial bd-oxidase) as variant_sets. The gene-by-gene reviews remain the
source of concrete subunit grounding that a future organism-specific module can
specialize from.

Validate with:

uv run linkml-validate -s src/ai_gene_review/schema/gene_review.yaml -C ModuleReview modules/oxphos.yaml

Model Species

Primary: Homo sapiens (human)

Annotation Review Focus

Key annotation issues in OXPHOS genes:
- Assembly factors should be annotated to assembly processes, NOT electron transport directly
- Dual-function proteins (e.g., SDHA in both TCA cycle and ETC) need both roles annotated
- Tissue-specific isoforms may warrant distinct annotations
- Supercomplex/respirasome assembly is a distinct process from individual complex assembly
- SDH subunit tumor suppressor roles (oncometabolite mechanism) vs. metabolic function
- Avoid generic "protein binding" for assembly factor interactions

Complex I -- NADH:ubiquinone oxidoreductase

The largest ETC complex (~1 MDa, 44 subunits). 7 mtDNA-encoded + 37 nuclear-encoded.
Transfers electrons from NADH to ubiquinone, pumping 4 H+ per NADH.

Core catalytic subunits (Priority 1)

Key accessory subunits (Priority 2)

Key assembly factors (Priority 2)

Complex II -- Succinate dehydrogenase

Only entirely nuclear-encoded ETC complex. Participates in both TCA cycle and ETC.
Does NOT pump protons. Tumor suppressor role via oncometabolite mechanism.

All subunits (Priority 1)

Assembly factors (Priority 2)

Complex III -- Cytochrome bc1

Homodimer (III2), 11 subunits per monomer. Transfers electrons from ubiquinol to
cytochrome c via Q-cycle, pumping 4 H+ per QH2.

Core catalytic subunits (Priority 1)

Key assembly factors (Priority 2)

Complex IV -- Cytochrome c oxidase

Terminal oxidase. 14 subunits. Transfers electrons from cytochrome c to O2, pumping 4 H+.

Core subunits (Priority 1)

Key assembly factors (Priority 1-2)

Complex V -- ATP synthase

Rotary motor enzyme. Uses proton gradient to synthesize ATP (~4 H+/ATP).
F1 (catalytic) + Fo (proton channel) + central/peripheral stalks.

Core subunits (Priority 1)

Key assembly factors (Priority 2)

Mobile Electron Carriers and Accessory Proteins

Cytochrome c (Priority 1)

CoQ10 Biosynthesis (Priority 2-3)

ETF system (Priority 3)

Supercomplex (Priority 3)

Disease Context

• Leigh syndrome: >100 genes; NDUFS4, SURF1, MT-ATP6 most common
• LHON: MT-ND4, MT-ND1, MT-ND6 (Complex I, mtDNA)
• MELAS/MERRF: tRNA mutations affecting multiple complexes
• Paraganglioma/pheochromocytoma: SDHA/B/C/D, SDHAF2 (tumor suppressors)
• CoQ10 deficiency: COQ2-9, PDSS1/2
• GRACILE syndrome: BCS1L (Complex III)
• Barth syndrome: TAZ (cardiolipin, indirect)

Priority Gene List for Review

Focus on nuclear-encoded genes with rich GO annotation to review.
mtDNA-encoded genes have limited GO annotations and are lower priority.

Tier 1 (High Priority) -- Core catalytic, disease-relevant, annotation-rich:
1. SDHA -- dual TCA/ETC function, tumor suppressor
2. SDHB -- tumor suppressor, Fe-S subunit
3. CYCS -- dual ETC/apoptosis function
4. NDUFS1 -- largest CI subunit, Fe-S chain
5. NDUFV1 -- NADH binding, primary electron entry
6. UQCRFS1 -- Rieske protein, catalytic
7. ATP5F1B -- catalytic beta subunit
8. SURF1 -- most common COX assembly defect
9. ATP5IF1 -- regulatory inhibitor

Tier 2 (Medium Priority) -- Important structural/assembly:
10. NDUFS2 -- ubiquinone binding
11. NDUFS4 -- Leigh syndrome, regulatory
12. SDHC -- membrane anchor, tumor suppressor
13. SDHD -- membrane anchor, tumor suppressor
14. UQCRC1 -- Complex III core protein
15. COX4I1 -- regulatory subunit
16. NDUFA4 -- reclassified CI->CIV
17. BCS1L -- GRACILE syndrome
18. SCO2 -- copper delivery
19. ACAD9 -- dual function (CI assembly + FAD)
20. ATP5F1A -- F1 alpha subunit

Tier 3 (Lower Priority) -- Specialized/accessory:
21. SDHAF2 -- paraganglioma
22. COQ8A -- cerebellar ataxia
23. ETFDH -- FAO electron entry to ETC
24. COX7A2L -- supercomplex assembly (controversial)
25. HCCS -- heme maturation

STATUS

• [x] CYC1 -- already reviewed
• [x] COX5B -- already reviewed
• [x] ATP5MC1 -- already reviewed
• [x] ATP5MC2 -- already reviewed
• [x] ATP5MC3 -- already reviewed
• [x] TMEM70 -- already reviewed
• [x] LRPPRC -- already reviewed
• [x] COX4I1 -- already reviewed
• [x] NDUFA4 -- already reviewed
• [x] SCO2 -- already reviewed
• [x] SDHA -- reviewed 2026-02-11 (56 annotations, core_functions with contributes_to)
• [x] SDHB -- reviewed 2026-02-11 (49 annotations, tumor suppressor role documented)
• [x] CYCS -- reviewed 2026-02-11 (53 annotations, dual ETC/apoptosis core_functions)
• [x] NDUFS1 -- reviewed 2026-02-11 (57 annotations, Fe-S electron relay, contributes_to CI activity)
• [x] NDUFV1 -- reviewed 2026-02-11 (44 annotations + 2 NEW, FMN catalytic subunit, NADH dehydrogenase activity)
• [x] UQCRFS1 -- reviewed 2026-02-11 (31 annotations + 1 NEW, Rieske Fe-S electron transfer, contributes_to CIII activity)
• [x] ATP5F1B -- reviewed 2026-02-11 (89 annotations, catalytic beta subunit, ecto-ATP synthase as non-core)
• [x] SURF1 -- reviewed 2026-02-11 (19 annotations + 1 NEW, CIV assembly factor, root MF)
• [x] ATP5IF1 -- reviewed 2026-02-11 (49 annotations + 1 NEW, ATPase inhibitor activity, pH-dependent)
• [x] COX4I2 -- reviewed 2026-05-18 (21 annotations, non-catalytic COX4 isoform, contributes_to CIV activity)
• [x] COX6A1 -- reviewed 2026-05-18 (19 annotations, regulatory/supernumerary CIV subunit)
• [x] COX6B1 -- reviewed 2026-05-18 (20 annotations, structural CIV subunit; cytochrome-c oxidase MF over-attributed)
• [x] SCO1 -- reviewed 2026-05-18 (24 annotations, copper chaperone/COX2 CuA maturation factor)
• [x] COX10 -- reviewed 2026-05-18 (24 annotations, heme O synthase; erroneous GO:0004311 assignment removed)
• [x] COX15 -- reviewed 2026-05-18 (25 annotations, heme A synthase; complex-component calls over-annotated)
• [ ] NDUFS2
• [ ] NDUFS4
• [ ] SDHC
• [ ] SDHD
• [ ] UQCRC1
• [ ] BCS1L
• [ ] ACAD9
• [ ] ATP5F1A
• [ ] SDHAF2
• [ ] COQ8A
• [ ] ETFDH
• [ ] COX7A2L
• [ ] HCCS

NOTES

2026-06-20

Added a generic, taxon-neutral OXPHOS module at modules/oxphos.yaml
(ModuleReview, validates cleanly). Key modelling decision ("how we put in
complexes"): each respiratory complex is one PROTEIN_COMPLEX node whose
emergent catalytic activity is a single complex-level annoton, with subunits as
active_units (mirroring GO contributes_to) rather than per-subunit annotons;
Complex I and the ATP synthase are additionally decomposed into functional
sub-modules (N/Q/P arms; F1 head + Fo turbine). Mobile carriers (quinone pool,
cytochrome c) are MOLECULAR_FUNCTION carrier nodes; auxiliary quinone-reducing
dehydrogenases (ETF-QO, mGPDH, DHODH) feed the pool. Lineage alternatives
(NDH-2, AOX, bd-oxidase) are variant_sets; supercomplex/respirasome
organization and complex biogenesis are optional sub-modules. ETC -> ATP
synthase is a chemiosmotic PRECEDES coupling, not a metabolite hand-off.

2026-05-18

Completed the pending Complex IV curation batch: COX4I2, COX6A1, COX6B1, SCO1,
COX10, and COX15. All six validate cleanly.

COX4I2/COX6A1/COX6B1 use the Complex IV subunit pattern: keep respiratory chain
Complex IV membership and cytochrome-c-to-oxygen electron transport, but separate
whole-complex cytochrome-c oxidase activity into contributes_to_molecular_function
for non-catalytic subunits. COX6B1's direct cytochrome-c oxidase activity annotation
was marked over-annotated rather than accepted as an individual subunit activity.

SCO1 was curated as a copper chaperone/COX2 CuA-site maturation factor, matching the
SCO2 pattern. COX10 and COX15 were curated as heme A biosynthesis enzymes rather
than mature Complex IV components: COX10 as protoheme IX farnesyltransferase/heme O
synthase, COX15 as heme A synthase. COX10's GO:0004311 annotations were removed as
wrong-reaction MF assignments.

2026-02-11

Completed first 3 Tier 1 reviews (SDHA, SDHB, CYCS). Key findings:
- SDHA: catalytic flavoprotein with contributes_to SDH quinone activity. First gene to use
new contributes_to_molecular_function schema field for complex subunit pattern.
- SDHB: iron-sulfur relay subunit, tumor suppressor via oncometabolite mechanism documented.
- CYCS: dual-function gene with 2 core_functions entries (ETC electron carrier + apoptosis).
Added NEW GO:0043293 (apoptosome). Corrected GO:0097194->GO:0097193 (intrinsic signaling,
not execution phase).

Fetched and prepared remaining Tier 1 genes (NDUFS1, NDUFV1, UQCRFS1, ATP5F1B, SURF1, ATP5IF1).
Deep research completed for all 6. NDUFS1 and NDUFV1 annotation reviews completed.

NDUFS1 (57 ann): 75 kDa Fe-S subunit, largest CI subunit. N-module, electron relay via 3 Fe-S
clusters. enables GO:0009055 (electron transfer), contributes_to GO:0008137 (CI activity).
Caspase cleavage role (PMID:15186778) documented as non-core. MDM2 interaction (PMID:30879903).

NDUFV1 (44 ann + 2 NEW): 51 kDa FMN catalytic subunit, primary NADH acceptor. N-module tip.
NEW GO:0003954 (NADH dehydrogenase activity, enables) -- subunit-specific MF analogous to SDHA
pattern. NEW GO:0009055 (electron transfer activity). contributes_to GO:0008137 (CI activity).
Cdk1 phosphorylation for G2/M cell cycle (PMID:24746669) documented.

Completed remaining 4 Tier 1 reviews (UQCRFS1, ATP5F1B, SURF1, ATP5IF1). All Tier 1 done.

UQCRFS1 (31 ann + 1 NEW): Rieske iron-sulfur protein, Complex III catalytic subunit. [2Fe-2S]
electron transfer from QH2 to cytochrome c1. NEW GO:0009055 (electron transfer activity).
contributes_to GO:0008121 (quinol-cytochrome-c reductase activity). Assembly pathway via
LYRM7/HSC20/HSPA9/BCS1L documented. Complex III assembly (GO:0034551) kept as non-core.

ATP5F1B (89 ann): F1 catalytic beta subunit, largest review in project. contributes_to
GO:0046933 (proton-transporting ATP synthase, rotational). Extensive ecto-ATP synthase
annotations (angiogenesis, MHC class I binding, cell surface) all KEEP_AS_NON_CORE.
Multiple protein binding annotations over-annotated.

SURF1 (19 ann + 1 NEW): Complex IV assembly factor, most common COX-related Leigh syndrome.
NEW GO:0062011 (CIV pre-assembly complex). Assembly factor pattern: root MF (GO:0003674)
since molecular function not fully characterized. Removed incorrect cytochrome-c oxidase
activity and proton transport annotations.

ATP5IF1 (49 ann + 1 NEW): IF1 inhibitory factor, prevents futile ATP hydrolysis. Core MF
GO:0042030 (ATPase inhibitor activity). NEW GO:0005759 (mitochondrial matrix). pH-dependent
dimerization mechanism. 8 MODIFY actions improving term specificity. Heme biosynthesis role
(PMID:23135403) documented as non-core.

2026-02-10

Project created. OXPHOS gene annotation review covering all five respiratory chain complexes
plus mobile electron carriers and assembly factors. 7 genes already reviewed from prior
projects (ATP5MC1/2/3, CYC1, COX5B, TMEM70, LRPPRC). 25 new genes prioritized across
three tiers. Complex II (SDH) genes are particularly interesting due to dual TCA/ETC
function and tumor suppressor roles.