Photosynthesis

Concept notes, a taxon-neutral module, and a candidate-gene checklist

AI Gene Review · projects/PHOTOSYNTHESIS · 2026

Bottom line

  • Oxygenic photosynthesis moves electrons from water → PSII → cyt b6f → PSI → NADP+ and spends NADPH + ATP fixing CO2 in the CBB cycle.
  • First pass done: concept notes, falcon deep research, a DRAFT photosynthesis module, and a checklist over 7 functional modules.
  • Gene reviews have not started beyond three Chlamydomonas genes already in the repo: psaC (complete), CP12 (draft), LCI5.

What the module covers

Why concept first

  • Photosynthesis spans cyanobacteria, algae and plants; no single organism is best for every part.
  • Mixed strategy: Synechocystis (SYNY3) for reaction centres, Chlamydomonas (CHLRE) for CBB and CO2 concentration, Arabidopsis (ARATH) for antenna and photoprotection.
  • Fixing the GO representation first avoids wrong-organism accessions and generic terms later.

Annotation watch-points

  • Prefer GO:0019253 reductive pentose-phosphate cycle over broad GO:0015977 carbon fixation for CBB enzymes.
  • Reaction-centre subunits often inherit GO:0009765 light harvesting or GO:0016168 chlorophyll binding from pipelines: consider over-annotated / modify.
  • Non-catalytic structural subunits (e.g. PsbO) may inherit catalytic MF terms from family rules.

The module

modules/photosynthesis.yaml (DRAFT): light reactions, CBB cycle, photoprotection, CCM and pigment supply; identifiers grounded only where verified.

The three seeded reviews

Gene Status Rows Outcome
psaC (PSI Fe-S subunit) COMPLETE 9 5 accept, 2 over-annotated, 2 removed (generic metal ion binding, oxidoreductase)
CP12 (CBB redox switch) DRAFT 11 6 accept, 2 non-core, 3 protein binding → enzyme binding
LCI5 (CCM thylakoid protein) — 0 no GOA rows; 7 terms proposed

Status and next steps

  • ✅ Concept notes, deep research, DRAFT module.
  • ⬜ Module A PSII: psbA, psbD, psbB/C, psbO · Module B PSI: psaA/B
  • ⬜ Module C electron transport: petA/B/C, petE, petF, petH, atpA/B
  • ⬜ Modules D–G: LHCB1, PsbS; rbcL/S, rca, PRK, GAPDH; LCIA/B, CCM1; CHLH, POR

Read more: projects/PHOTOSYNTHESIS.md · modules/photosynthesis.yaml · terms/photosynthesis/