Photosynthesis Project
Overview
Photosynthesis is the light-driven assimilation of CO2 into organic carbon. In oxygenic
photosynthesis (cyanobacteria, algae, plants) light energy captured by chlorophyll drives
electron transport from water to NADP+, producing NADPH, ATP, and O2 (the light
reactions), which then power the Calvin–Benson–Bassham reductive pentose-phosphate cycle
to fix CO2 (carbon fixation). It is arguably the most important biochemical process in
the biosphere and a major target for crop-improvement and synthetic-biology research.
Concept-level research notes (definitions, GO representation, full component breakdown, and
verified references) live in terms/photosynthesis/photosynthesis-notes.md.
Scope of this first pass
Per the chosen scope, this pass delivers the concept writeup plus a candidate-gene
checklist; individual gene reviews are deferred. Strategy: mix across organisms,
choosing the best-characterized ortholog per functional module.
Model species selection (mixed strategy)
- Cyanobacteria — Synechocystis sp. PCC 6803 (UniProt species code SYNY3*,
taxonomy 1148) and/or Thermosynechococcus***: cleanest genetics for the core light
reactions; source organisms for the landmark PSI and PSII crystal structures. Preferred
for reaction-center and electron-transport subunits. - Green alga — Chlamydomonas reinhardtii (CHLRE, taxonomy 3055): already seeded
in this repo (psaC, CP12, LCI5); strong for CBB-cycle regulation and the
carbon-concentrating mechanism. - Land plant — Arabidopsis thaliana (ARATH): preferred for photoprotection
(PsbS), the LHC antenna family, and nuclear-encoded Rubisco small subunit / activase. - Reference structural orthologs (spinach / tobacco Rubisco; Thermosynechococcus
PSII) where a module is best characterized elsewhere.
Functional modules and candidate genes
Accessions are listed only where verified in this repository; others should be resolved
with just fetch-gene <organism> <gene> when each review starts (this avoids the
wrong-organism accession pitfalls seen in earlier projects).
Module A — Photosystem II (water oxidation)
| Gene | Suggested organism | Role |
|---|---|---|
| psbA (D1) | SYNY3 / plant chloroplast | reaction-center, binds P680 + Mn4CaO5 cluster |
| psbD (D2) | SYNY3 | reaction-center, partners D1 |
| psbB (CP47) / psbC (CP43) | SYNY3 | core chlorophyll antenna |
| psbO | ARATH / SYNY3 | oxygen-evolving complex extrinsic protein (GO:0009654) |
Module B — Photosystem I
| Gene | Suggested organism | Role |
|---|---|---|
| psaA / psaB | SYNY3 | reaction-center heterodimer, binds P700 |
| psaC | CHLRE (Q00914) — already seeded | terminal FA/FB Fe-S clusters |
Module C — Electron transport & coupling
| Gene | Suggested organism | Role |
|---|---|---|
| petA / petB / petC | SYNY3 | cytochrome b6f complex (Q-cycle, proton translocation) |
| petE | SYNY3 / ARATH | plastocyanin (mobile Cu carrier) |
| petF | CHLRE / ARATH | ferredoxin (mobile Fe-S carrier) |
| petH (FNR) | ARATH | ferredoxin–NADP+ reductase (makes NADPH) |
| atpA / atpB | SYNY3 / plant chloroplast | chloroplast ATP synthase CF1 |
Module D — Light harvesting & photoprotection
| Gene | Suggested organism | Role |
|---|---|---|
| LHCB1 / LHCA | ARATH / CHLRE | chlorophyll a/b-binding antenna |
| PsbS | ARATH | non-photochemical quenching (qE) photoprotection |
Module E — Carbon fixation (Calvin–Benson–Bassham cycle)
| Gene | Suggested organism | Role |
|---|---|---|
| rbcL | tobacco/spinach chloroplast or SYNY3 | Rubisco large (catalytic) subunit (GO:0016984) |
| rbcS | ARATH | Rubisco small subunit |
| rca | ARATH | Rubisco activase |
| prk (PRK) | CHLRE / ARATH | phosphoribulokinase (regenerates RuBP) |
| gapA / gapB | ARATH | chloroplastic GAPDH (redox-regulated) |
| CP12 | CHLRE (A6Q0K5) — already seeded | redox switch; PRK–GAPDH–CP12 ternary complex |
Module F — Carbon-concentrating mechanism (algae/cyano)
| Gene | Suggested organism | Role |
|---|---|---|
| LCI5 | CHLRE (Q94ET8) — already seeded | low-CO2 inducible thylakoid protein |
| LCIA / LCIB, CCM1/CIA5, carbonic anhydrases | CHLRE / SYNY3 | inorganic-carbon uptake/concentration |
Module G — Pigment biosynthesis (supporting context)
| Gene | Suggested organism | Role |
|---|---|---|
| CHLH / CHLD / CHLI | ARATH | magnesium chelatase (committed chlorophyll step) |
| POR | ARATH | protochlorophyllide oxidoreductase |
Annotation watch-points (apply during review)
- Prefer
GO:0019253(reductive pentose-phosphate cycle) over the broadGO:0015977
(carbon fixation) for CBB-cycle enzymes. - Reaction-center subunits often inherit generic
GO:0009765(light harvesting) or
GO:0016168(chlorophyll binding) from electronic pipelines — consider
MARK_AS_OVER_ANNOTATED/MODIFYtoward charge-separation / electron-transport terms. - Non-catalytic structural subunits (e.g. PsbO) may inherit catalytic MF terms from
family rules — flag as the cellulosome project did for scaffoldins.
Why study photosynthesis?
- Food security / crop yield — Rubisco efficiency and CBB-cycle engineering.
- Climate / carbon cycle — primary route of CO2 fixation into the biosphere.
- Bioenergy & synthetic biology — engineered carbon-concentrating mechanisms,
artificial photosynthesis. - Basic science — model supramolecular machines (PSI/PSII) and redox signalling (CP12).
Key references
According to PubMed (verified):
- Umena et al. 2011, Nature 473:55–60 — PSII 1.9 Å structure. PMID:21499260.
- Jordan et al. 2001, Nature 411:909–917 — PSI 2.5 Å structure. PMID:11418848.
- Andersson & Backlund 2008, Plant Physiol Biochem 46:275–291 — Rubisco. PMID:18294858.
- Shao et al. 2021, Cell Commun Signal 19:38 — CP12 / CBB regulation. PMID:33761918.
STATUS
Concept writeup
- [x]
terms/photosynthesis/photosynthesis-notes.mdcreated (manual notes) - [x] GO representation verified against
cache/go/terms.csv+ GOlr - [x] Key references PubMed-verified
- [x] Automated deep research
photosynthesis-deep-research-falcon.md(falcon; generated after the template fix; machine citations not yet manually adjudicated) - [x] Structured module curated:
modules/photosynthesis.yaml(validates againstModuleReview; light reactions + CBB cycle + photoprotection/CCM/pigment supply; GO IDs and UniProt members grounded only where verified)
Gene reviews (deferred — first pass is concept writeup only)
Already seeded
- [x] CHLRE/psaC (Q00914) — pre-existing
- [~] CHLRE/CP12 (A6Q0K5) — pre-existing (DRAFT)
- [~] CHLRE/LCI5 (Q94ET8) — pre-existing
To do (candidates)
- [ ] Module A — PSII: psbA, psbD, psbB/psbC, psbO
- [ ] Module B — PSI: psaA, psaB
- [ ] Module C — electron transport: petA/B/C, petE, petF, petH, atpA/atpB
- [ ] Module D — antenna/photoprotection: LHCB1, PsbS
- [ ] Module E — CBB cycle: rbcL, rbcS, rca, PRK, gapA/gapB
- [ ] Module F — CCM: LCIA/B, CCM1, carbonic anhydrases
- [ ] Module G — pigment biosynthesis: CHLH, POR
NOTES
2026-06-12 (Session 1)
Project created. Scope for this pass: concept writeup + candidate-gene checklist;
individual reviews deferred. Mixed-organism strategy chosen (Synechocystis for core light
reactions, Chlamydomonas for CBB/CCM — already partly seeded — and Arabidopsis for
antenna/photoprotection and nuclear CBB genes).
Attempted just term-deep-research-falcon "Photosynthesis"; the provider run failed
because templates/concept_research.md.j2 embeds a literal {concept} placeholder that is
not substituted, so the model received an empty concept and returned a "cannot be
completed" non-report. The empty file was discarded (not kept as
-deep-research-falcon.md) and terms/photosynthesis/photosynthesis-notes.md was authored
manually instead, with all GO IDs and PMIDs independently verified.
Follow-up infra note (RESOLVED 2026-06-14): templates/concept_research.md.j2 is
detected as a Jinja template (.j2 suffix) but used a literal f-string placeholder
{concept}, which Jinja leaves untouched — so every concept deep-research run received an
empty concept. Fixed by switching the placeholder to Jinja syntax {{ concept }}; verified
by rendering through TemplateProcessor (now substitutes to the real concept).