Oxygenic photosynthesis module

A taxon-neutral decomposition of oxygenic photosynthesis as a recursively decomposable module. The module separates the thylakoid light reactions (light harvesting, water oxidation at photosystem II, the cytochrome b6f complex, photosystem I, mobile electron carriers, ferredoxin-NADP+ reductase, and the ATP synthase) from carbon fixation by the Calvin-Benson-Bassham reductive pentose-phosphate cycle, and adds optional photoprotection/electron balancing, the inorganic carbon-concentrating mechanism, and chlorophyll supply. It is phrased as functions, complexes, and pathway segments rather than a fixed gene list so it can represent cyanobacterial, algal, and plant implementations. Anoxygenic photosynthesis (single reaction center, non-water electron donors) is explicitly out of scope.

MODULE:oxygenic_photosynthesisDRAFTBiological Processmodules/photosynthesis.yaml
oxygenic photosynthesisGO:0015979
file:modules/photosynthesis-deep-research-falcon.md
Photosynthesis module deep research (falcon)
Module-targeted falcon deep research (generated from this module's outline) used to cross-check component coverage, variants, and failure modes. Machine-generated citations are not yet manually adjudicated.
file:terms/photosynthesis/photosynthesis-deep-research-falcon.md
Photosynthesis concept deep research (falcon)
Falcon deep-research synthesis used to set module boundaries and the module-by-module component breakdown across Arabidopsis, Synechocystis, and Chlamydomonas (core vs accessory vs regulatory factors).
file:terms/photosynthesis/photosynthesis-notes.md
Photosynthesis concept notes
Manually authored, GO- and PubMed-verified concept notes underpinning this module.
GO:0015979
photosynthesis
The module is grounded in the GO biological-process term for photosynthesis.
PMID:21499260
Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 A
Defines the PSII D1/D2 reaction center, CP43/CP47 inner antennae, and the Mn4CaO5 water-oxidation cluster stabilized by the extrinsic OEC proteins.
PMID:11418848
Three-dimensional structure of cyanobacterial photosystem I at 2.5 A resolution
Defines the PsaA/PsaB reaction-center heterodimer and the terminal Fe-S clusters carried by PsaC.
PMID:18294858
Structure and function of Rubisco
Supports Rubisco as the major carboxylating enzyme of the CBB cycle and its competing oxygenase side-reaction.
PMID:33761918
A new type of flexible CP12 protein in the marine diatom Thalassiosira pseudonana
Supports CP12 as a redox-controlled scaffold that forms a PRK-GAPDH-CP12 ternary complex regulating the CBB cycle.
PMID:37549282
NTRC regulates CP12 to activate Calvin-Benson cycle during cold acclimation
Supports redox (NTRC/thioredoxin)-dependent assembly/disassembly of the PRK-CP12-GAPDH supracomplex gating CBB-cycle activity.

Identifiers are grounded only where verified against the local GO term cache, GOlr, or UniProt; descriptors without a `term` are deliberate (no confident identifier yet) rather than oversights. Representative UniProt members are concrete orienting examples, not exhaustive or species-restricting claims.

25Nodes
17Parts
3Variant Sets
7Variants
22Annotons
9Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✓ present

  • photosynthesis-deep-research-falcon.md (falcon)

Leaf nodes lacking representative members

14 leaf node(s) with no concrete protein grounding:

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Gene-review completeness (3/6 grounded genes reviewed)

3 complete review(s) · 3 with deep research · 3 missing review · 0 reviewed but lacking deep research

Gene Review Complete Deep research
CP12 A6Q0K5 ✓ ✓ ✓
LCI5 Q94ET8 ✓ ✓ ✓
spinach PsbO (oxygen-evolving enhancer protein 1) P12359 ✗ — —
Synechocystis cytochrome f (petA) P26287 ✗ — —
psaC Q00914 ✓ ✓ ✓
wheat Rieske Fe-S subunit (petC) Q7X9A6 ✗ — —

Details

Context
cyanobacteria eukaryotic algae land plants
photosynthetic membraneGO:0034357
Oxygenic photosynthesisBiological Processoxygenic_photosynthesis
oxygenic photosynthesisGO:0015979
Context
cyanobacteria eukaryotic algae land plants
photosynthetic membraneGO:0034357

Concrete organism modules can specialize abstract participants with specific genes, complexes, compartments, and transporters (e.g. Synechocystis psbA/ psaA, Chlamydomonas pyrenoid CCM, Arabidopsis PsbS/RbcS) without the generic module naming every protein.

Connections

light_reactions -> carbon_fixation Provides Input For
The light reactions supply the ATP and NADPH consumed by the Calvin-Benson-Bassham cycle.
The CCM raises CO2 around Rubisco, favoring carboxylation over oxygenation.
Part 1: light reactions (electron transport and photophosphorylation)
Thylakoid light reactionsBiological Processlight_reactions
photosynthesis, light reactionGO:0019684 photosynthetic electron transport chainGO:0009767

Connections

photosystem_II -> cytochrome_b6f Provides Input For
PSII reduces plastoquinone to plastoquinol, the substrate oxidized by b6f.
b6f reduces the mobile lumenal carrier (plastocyanin or cyt c6).
The reduced carrier re-reduces photo-oxidized P700 in PSI.
photosystem_I -> fnr_step Provides Input For
PSI-reduced ferredoxin is the electron donor for FNR.
fnr_step -> atp_synthase Precedes
Linear electron flow and water oxidation build the proton-motive force used by the ATP synthase (coupling, not a metabolite hand-off).
Part 1: light harvesting / antenna
Light-harvesting antennaMolecular Functionlight_harvesting

Annotons

Antenna chlorophyll/carotenoid light capture
antenna_chlorophyll_binding
Participant: Family: light-harvesting chlorophyll a/b binding (LHC) family
Family:
light-harvesting chlorophyll a/b binding (LHC) family Membrane antenna proteins (LHCII/LHCI in plants and algae; phycobilisomes substitute in most cyanobacteria).

Function

chlorophyll binding for excitation energy transferGO:0016168
Cofactors: chlorophyll a chlorophyll b carotenoid

Locations

thylakoid membraneGO:0034357

Increases absorption cross-section and funnels excitation to the reaction centers; also a site of photoprotective quenching.

Part 2: water oxidation (photosystem II)
Photosystem II (water:plastoquinone oxidoreductase)Protein Complexphotosystem_II
photosystem IIGO:0009523

Annotons

Light-driven water oxidation / oxygen evolution
psii_water_oxidation
Participant: Protein Complex: photosystem II complex
Protein Complex:
photosystem II complexGO:0009523
Active units:
D1 reaction-center subunit (PsbA)
Participant: Family: PsbA / D1
Family:
PsbA / D1
Role: binds P680 and the Mn4CaO5 cluster; high-turnover repair substrate
D2 reaction-center subunit (PsbD)
Participant: Family: PsbD / D2
Family:
PsbD / D2
Role: reaction-center partner of D1
Core antennae CP43/CP47 (PsbC/PsbB)
Participant: Family: PsbB/PsbC core antenna
Family:
PsbB/PsbC core antenna
Role: inner chlorophyll antennae feeding excitation to P680
Oxygen-evolving complex extrinsic proteins (PsbO/PsbP/PsbQ)
Participant: Family: oxygen-evolving complex extrinsic proteins
Family:
oxygen-evolving complex extrinsic proteins
Representative Members: spinach PsbO (oxygen-evolving enhancer protein 1)UniProtKB:P12359
Role: stabilize the Mn4CaO5 water-oxidation cluster on the lumenal side

Function

oxygen evolving activityGO:0010242
Substrates: water plastoquinone
Products: dioxygen plastoquinol proton (lumen)

Locations

thylakoid membrane / oxygen-evolving complexGO:0009654

Uses light energy to oxidize water at the Mn4CaO5 cluster, reducing plastoquinone and releasing O2 and lumenal protons.

PMID:21499260
PSII structure defining the reaction center, antennae, and Mn4CaO5 cluster.
Part 3: plastoquinol oxidation and proton translocation (cytochrome b6f)
Cytochrome b6f complexProtein Complexcytochrome_b6f
cytochrome b6f complexGO:0009512

Annotons

Plastoquinol--plastocyanin reductase (Q-cycle)
b6f_plastoquinol_plastocyanin_reductase
Participant: Protein Complex: cytochrome b6f complex
Protein Complex:
cytochrome b6f complexGO:0009512
Active units:
Cytochrome f (PetA)
Participant: Family: cytochrome f (PetA)
Family:
cytochrome f (PetA)
Representative Members: Synechocystis cytochrome f (petA)UniProtKB:P26287
Role: high-potential heme; reduces plastocyanin/cyt c6
Cytochrome b6 (PetB)
Participant: Family: cytochrome b6 (PetB)
Family:
cytochrome b6 (PetB)
Role: low-potential hemes; Q-cycle electron bifurcation
Rieske iron-sulfur protein (PetC)
Participant: Family: Rieske Fe-S protein (PetC)
Family:
Rieske Fe-S protein (PetC)
Representative Members: wheat Rieske Fe-S subunit (petC)UniProtKB:Q7X9A6
Role: 2Fe-2S cluster; oxidizes plastoquinol

Function

plastoquinol--plastocyanin reductase activityGO:0009496
Substrates: plastoquinol plastocyanin (oxidized)
Products: plastoquinone plastocyanin (reduced) proton (lumen)

Locations

thylakoid membraneGO:0009535

Links PSII to PSI, oxidizing plastoquinol and reducing the mobile carrier while translocating protons via the Q-cycle; frequently rate-limiting for linear electron transport.

Part 4: inter-photosystem mobile electron carrier
Mobile carrier from b6f to PSIMolecular Functionmobile_carrier_b6f_to_psi

Soluble lumenal carrier shuttling electrons from cytochrome b6f to photosystem I; the carrier used is lineage- and metal-availability-dependent.

Variant set: Plastocyanin vs cytochrome c6 by lineage / metal availability (Exactly One)

Many cyanobacteria and algae switch between plastocyanin and cytochrome c6 depending on copper/iron availability.

Plastocyanin (copper carrier)Molecular Functionplastocyanin_variant

Annotons

Plastocyanin electron transfer
plastocyanin_electron_transfer
Participant: Family: plastocyanin
Family:
plastocyanin

Function

electron transfer activityGO:0009055
Cofactors: copper ion

Locations

thylakoid lumenGO:0009543
Cytochrome c6 (iron carrier)Molecular Functioncytochrome_c6_variant

Annotons

Cytochrome c6 electron transfer
cytc6_electron_transfer
Participant: Family: cytochrome c6
Family:
cytochrome c6

Function

electron transfer activityGO:0009055
Cofactors: heme c

Locations

thylakoid lumenGO:0031977
Part 5: P700 photo-oxidation and ferredoxin reduction (photosystem I)
Photosystem I (plastocyanin:ferredoxin oxidoreductase)Protein Complexphotosystem_I
photosystem IGO:0009522

Annotons

Light-driven ferredoxin reduction
psi_ferredoxin_reduction
Participant: Protein Complex: photosystem I complex
Protein Complex:
photosystem I complexGO:0009522
Active units:
PsaA/PsaB reaction-center heterodimer
Participant: Family: PsaA/PsaB reaction-center
Family:
PsaA/PsaB reaction-center
Role: bind P700 and early electron-transfer cofactors
PsaC terminal Fe-S clusters (FA/FB)
Participant: Family: PsaC
Family:
PsaC
Representative Members: Chlamydomonas psaCUniProtKB:Q00914
Role: terminal 4Fe-4S clusters that reduce ferredoxin

Function

light-driven plastocyanin:ferredoxin oxidoreduction Photo-oxidation of P700 drives electron transfer through Fe-S clusters to reduce ferredoxin; no single exact GO MF is asserted for the whole complex here.
Substrates: plastocyanin (reduced) or cytochrome c6 ferredoxin (oxidized)
Products: ferredoxin (reduced)

Processes

photosynthetic electron transport in photosystem IGO:0009773

Locations

thylakoid membraneGO:0009535
PMID:11418848
PSI structure defining PsaA/PsaB and terminal Fe-S clusters.
Part 6: NADPH production
Ferredoxin-NADP+ reductaseReactionfnr_step

Annotons

Ferredoxin-NADP+ reductase
fnr_activity
Participant: Any With Function: ferredoxin-NADP+ reductase activity
Required Function:
ferredoxin-NADP+ reductase activityGO:0004324

Function

ferredoxin-NADP+ reductase activityGO:0004324
Substrates: ferredoxin (reduced) NADP+
Products: ferredoxin (oxidized) NADPH
Part 7: ATP synthesis from the proton-motive force
Thylakoid (chloroplast/cyanobacterial) ATP synthaseProtein Complexatp_synthase
proton-transporting ATP synthase complexGO:0045259

Annotons

Proton-motive-force-driven ATP synthesis
photophosphorylation
Participant: Protein Complex: thylakoid ATP synthase (CF1FO)
Protein Complex:
thylakoid ATP synthase (CF1FO)GO:0045259

Function

proton-transporting ATP synthase activity, rotational mechanismGO:0046933
Substrates: ADP phosphate proton (lumen)
Products: ATP

Locations

thylakoid membraneGO:0009535
Part 2: carbon fixation (Calvin-Benson-Bassham cycle)
Calvin-Benson-Bassham reductive pentose-phosphate cycleMetabolic Pathwaycarbon_fixation
reductive pentose-phosphate cycleGO:0019253 carbon fixationGO:0015977
Part 1: carboxylation
Rubisco carboxylation of RuBPReactionrubisco_carboxylation

Annotons

Ribulose-bisphosphate carboxylase
rubisco_activity
Participant: Any With Function: ribulose-bisphosphate carboxylase activity
Required Function:
ribulose-bisphosphate carboxylase activityGO:0016984
Form I Rubisco (L8S8, RbcL+RbcS) in plants, algae, and cyanobacteria; form II (L2) in some bacteria/dinoflagellates.

Function

ribulose-bisphosphate carboxylase activityGO:0016984
Substrates: ribulose 1,5-bisphosphate CO2
Products: 3-phosphoglycerate

Locations

chloroplast stroma / cyanobacterial cytoplasmGO:0009570

Fixes CO2 onto RuBP. The competing oxygenase reaction with O2 produces 2-phosphoglycolate (the substrate of photorespiration).

PMID:18294858
Rubisco as the principal carboxylating enzyme with a competing oxygenase activity.
Part 2: reduction phase
Reduction of 3-phosphoglycerate to triose phosphateMetabolic Pathwaycbb_reduction_phase

ATP- and NADPH-consuming reduction of 3-phosphoglycerate via 1,3-bisphosphoglycerate to glyceraldehyde 3-phosphate (phosphoglycerate kinase + chloroplastic NADP-GAPDH).

Annotons

NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
cbb_gapdh
Participant: Family: chloroplastic GAPDH (GapA/GapB)
Family:
chloroplastic GAPDH (GapA/GapB)

Function

glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity NADPH-consuming reduction step; no confident exact GO MF id asserted here.
Substrates: 1,3-bisphosphoglycerate NADPH
Products: glyceraldehyde 3-phosphate NADP+
Part 3: regeneration phase
Regeneration of ribulose 1,5-bisphosphateMetabolic Pathwaycbb_regeneration_phase

Rearrangement of triose phosphates through transketolase, aldolase, fructose-1,6-bisphosphatase, and sedoheptulose-1,7- bisphosphatase, ending in phosphoribulokinase regeneration of RuBP.

Annotons

Phosphoribulokinase
cbb_prk
Participant: Any With Function: phosphoribulokinase activity
Required Function:
phosphoribulokinase activityGO:0008974

Function

phosphoribulokinase activityGO:0008974
Substrates: ribulose 5-phosphate ATP
Products: ribulose 1,5-bisphosphate ADP

Regenerates the Rubisco substrate; a major redox-regulated control point.

Bisphosphatase regeneration steps (FBPase, SBPase)
cbb_sbpase_fbpase
Participant: Family: chloroplast FBPase / SBPase
Family:
chloroplast FBPase / SBPase

Function

bisphosphatase regeneration steps Fructose-1,6-bisphosphatase and sedoheptulose-1,7- bisphosphatase; SBPase is a frequent yield-engineering target.
Part 4: Rubisco activation and inhibitor repair (optional)
Rubisco activase and inhibitor removalRegulatory Steprubisco_activation

Annotons

Rubisco activase
rubisco_activase
Participant: Family: Rubisco activase (Rca)
Family:
Rubisco activase (Rca)

Function

ATP-dependent removal of inhibitory sugar phosphates from Rubisco AAA+ chaperone-like remodeling of Rubisco active sites; thermolabile.

Restores catalytically competent Rubisco; major thermal-tolerance target.

Part 5: redox gating of the CBB cycle (optional)
CP12-mediated redox regulationRegulatory Stepcbb_redox_regulation

Annotons

CP12 redox scaffold
cp12_scaffold
Participant: Family: CP12
Family:
CP12
Representative Members: Chlamydomonas CP12UniProtKB:A6Q0K5

Function

redox-dependent scaffolding of the PRK-GAPDH-CP12 ternary complex In the dark/oxidizing conditions CP12 assembles an autoinhibitory PRK-GAPDH complex; reduction (thioredoxin/ NTRC) dissociates it to activate the cycle.
Targets: phosphoribulokinase glyceraldehyde-3-phosphate dehydrogenase

Couples CBB-cycle activity to the light/redox state of the chloroplast.

PMID:33761918
CP12 forms a PRK-GAPDH ternary complex regulating the CBB cycle.
PMID:37549282
NTRC-dependent redox control of the PRK-CP12-GAPDH supracomplex.

Connections

cp12_scaffold -> cbb_prk Negatively Regulates
CP12 inhibits PRK in the dark/oxidized state.
cp12_scaffold -> cbb_gapdh Negatively Regulates
CP12 inhibits GAPDH in the dark/oxidized state.
Part 3: photoprotection and ATP/NADPH balancing (optional)
Photoprotection and electron/energy balancingRegulatory Stepphotoprotection_balancing

Mechanisms that dissipate excess excitation, redistribute antennae, and tune the ATP:NADPH ratio under fluctuating light.

Variant set: Photoprotection and balancing mechanisms by regulatory mechanism (Zero Or More)
Non-photochemical quenching (qE)Regulatory Stepnpq_variant

Annotons

PsbS- and xanthophyll-cycle-dependent quenching
npq_psbs_xanthophyll
Participant: Family: PsbS and xanthophyll-cycle enzymes (VDE/ZEP)
Family:
PsbS and xanthophyll-cycle enzymes (VDE/ZEP)

Function

heat dissipation of excess PSII excitation

Rapid, reversible thermal dissipation protecting PSII under high light.

State transitionsRegulatory Stepstate_transitions_variant

Annotons

STN7/Stt7-dependent LHCII redistribution
state_transition_kinase
Participant: Family: state-transition kinase (STN7/Stt7) and TAP38/PPH1 phosphatase
Family:
state-transition kinase (STN7/Stt7) and TAP38/PPH1 phosphatase

Function

redox-controlled LHCII phosphorylation balancing PSII/PSI

Rebalances excitation between the photosystems via antenna migration.

Cyclic electron flow around PSIRegulatory Stepcyclic_electron_flow_variant

Annotons

PGR5/PGRL1- and NDH-dependent cyclic electron flow
cef_pgr5_ndh
Participant: Family: PGR5/PGRL1 and NDH(-1) complex
Family:
PGR5/PGRL1 and NDH(-1) complex

Function

cyclic electron transfer generating extra proton-motive force

Raises ATP:NADPH and contributes to photoprotection.

Part 4: inorganic carbon-concentrating mechanism (CCM) (optional)
Carbon-concentrating mechanismRegulatory Stepcarbon_concentrating_mechanism

Active inorganic-carbon uptake and CO2 concentration around Rubisco to suppress the oxygenase reaction; prominent in cyanobacteria and algae.

Annotons

Carbonic anhydrase (CO2/HCO3- interconversion)
ccm_carbonic_anhydrase
Participant: Any With Function: carbonate dehydratase activity
Required Function:
carbonate dehydratase activityGO:0004089

Function

carbonate dehydratase activityGO:0004089
Substrates: bicarbonate
Products: CO2 water
Variant set: CCM compartmentation strategy by lineage / compartment (Exactly One)
Cyanobacterial carboxysome CCMCellular Componentcarboxysome_ccm

Annotons

Carboxysome microcompartment with encapsulated Rubisco/CA
carboxysome_unit
Participant: Family: carboxysome shell and cargo (Ccm/Cso)
Family:
carboxysome shell and cargo (Ccm/Cso)

Bacterial microcompartment concentrating CO2 around Rubisco.

Algal pyrenoid CCMCellular Componentpyrenoid_ccm

Annotons

Pyrenoid and bicarbonate transporter network
pyrenoid_unit
Participant: Family: pyrenoid CCM components (HLA3, LCIA, LCI1, LCIB, CAH3, CCM1/CIA5)
Family:
pyrenoid CCM components (HLA3, LCIA, LCI1, LCIB, CAH3, CCM1/CIA5)
Representative Members: Chlamydomonas LCI5 (low-CO2-inducible protein)UniProtKB:Q94ET8

Eukaryotic algal biophysical CCM organized around the pyrenoid.

Part 5: chlorophyll supply (supporting context) (optional)
Chlorophyll biosynthesis (supporting)Metabolic Pathwaypigment_biosynthesis

Supplies the chlorophyll cofactors required by antennae and reaction centers.

Annotons

Magnesium chelatase (committed step)
mg_chelatase
Participant: Family: magnesium chelatase (CHLH/CHLD/CHLI)
Family:
magnesium chelatase (CHLH/CHLD/CHLI)

Function

magnesium chelatase activity Inserts Mg2+ into protoporphyrin IX; committed step toward chlorophyll. No confident GO MF id asserted here.
Protochlorophyllide reductase
por_reduction
Participant: Any With Function: protochlorophyllide reductase activity
Required Function:
protochlorophyllide reductase activityGO:0016630

Function

protochlorophyllide reductase activityGO:0016630
Substrates: protochlorophyllide
Products: chlorophyllide