id: MODULE:plant_seed_triacylglycerol_biosynthesis title: Plant seed triacylglycerol (oil) biosynthesis module description: >- A taxon-neutral decomposition of plant seed storage-oil (triacylglycerol, TAG) assembly as a recursively decomposable module. In developing oilseeds, acyl groups (produced by plastidial fatty acid synthesis and activated as acyl-CoA) are assembled onto a glycerol backbone at the endoplasmic reticulum by the glycerol-phosphate (Kennedy) pathway and packaged into cytosolic oil bodies (lipid droplets) stabilized by oleosins. The module separates (1) acylation of glycerol-3-phosphate to lysophosphatidic acid (GPAT), (2) acylation of LPA to phosphatidic acid (LPAAT), (3) dephosphorylation of PA to diacylglycerol (PAP), (4) the final acyl transfer to DAG forming TAG by two alternative routes - acyl-CoA-dependent (DGAT1/DGAT2) and acyl-CoA-independent (PDAT, using phospholipid acyl donors) - and (5) oil-body biogenesis and oleosin stabilization. It is phrased as functions and pathway segments rather than a fixed gene list so it can represent Arabidopsis and crop oilseeds (soybean, rapeseed/canola, oil palm, camelina); concrete UniProt members are Arabidopsis exemplars, not species-restricting claims. Plastidial de novo fatty acid synthesis, acyl-chain desaturation/modification, and TAG catabolism (lipolysis/beta-oxidation) are upstream/downstream and out of scope. As a bioenergy module, total TAG flux (DGAT/PDAT capacity), the acyl-CoA pool, and oil-body number/size (oleosin dosage) are the principal engineering levers for raising seed-oil yield for biodiesel and oleochemical feedstocks. status: DRAFT evidence: - source_id: GO:0019432 title: triglyceride biosynthetic process statement: >- The module is grounded in the GO biological-process term for triacylglycerol (triglyceride) biosynthesis. - source_id: GO:0010344 title: seed oilbody biogenesis statement: >- The packaging output of the module is the seed oil body, grounded in the GO biological-process term for seed oilbody biogenesis. - source_id: UniProtKB:Q8GWG0 title: Glycerol-3-phosphate acyltransferase 9 (AtGPAT9) statement: >- Arabidopsis exemplar ER GPAT catalyzing the first Kennedy-pathway acylation of glycerol-3-phosphate (GO:0004366, EC 2.3.1.15). - source_id: UniProtKB:Q8LG50 title: 1-acyl-sn-glycerol-3-phosphate acyltransferase 2 (AtLPAT2) statement: >- Arabidopsis exemplar LPAAT acylating lysophosphatidic acid at sn-2 to form phosphatidic acid (GO:0003841, EC 2.3.1.51). - source_id: UniProtKB:Q9SF47 title: Phosphatidate phosphatase PAH1 (AtPAH1) statement: >- Arabidopsis exemplar PA phosphatase dephosphorylating phosphatidic acid to diacylglycerol (GO:0008195, EC 3.1.3.4). - source_id: UniProtKB:Q9SLD2 title: Diacylglycerol O-acyltransferase 1 (AtDGAT1 / TAG1) statement: >- Arabidopsis exemplar acyl-CoA:diacylglycerol acyltransferase catalyzing the committed TAG-forming step (GO:0004144, EC 2.3.1.20); tag1 has reduced seed oil. - source_id: UniProtKB:Q9ASU1 title: Diacylglycerol O-acyltransferase 2 (AtDGAT2) statement: >- Arabidopsis exemplar of the DGAT2 family, a second acyl-CoA-dependent route to TAG (GO:0004144) with a preference for unusual acyl chains. - source_id: UniProtKB:Q9FNA9 title: Phospholipid:diacylglycerol acyltransferase 1 (AtPDAT1) statement: >- Arabidopsis exemplar of the acyl-CoA-independent route transferring an acyl group from phospholipid to DAG (GO:0046027, EC 2.3.1.158); PDAT1 is redundant with DGAT1 and jointly essential for oil. - source_id: UniProtKB:Q39165 title: Oleosin 21.2 kDa / OLEO2 (AtOLEO2) statement: >- Arabidopsis exemplar seed oleosin coating the oil body and controlling its size and stability (lipid droplet, GO:0005811). notes: >- Identifiers are grounded only where verified against the local GO term cache or UniProt; descriptors without a `term` (e.g. acyl-CoA donor, glycerolipid intermediates) are deliberate rather than oversights. The final TAG step is represented as a variant set because plants use two mechanistically distinct routes - acyl-CoA-dependent DGAT1/DGAT2 and acyl-CoA-independent PDAT1 - that are genetically redundant in Arabidopsis (dgat1 pdat1 double mutants are pollen/seed lethal for oil). Some DAG can also be recruited from the phosphatidylcholine acyl-editing pool rather than solely de novo PAP output; that acyl-editing cycle is acknowledged but not expanded here. Representative UniProt members are concrete Arabidopsis exemplars for orientation, not exhaustive or species-restricting; crop oilseeds use orthologous machinery. module: id: plant_seed_triacylglycerol_biosynthesis label: Plant seed triacylglycerol (oil) biosynthesis module_type: METABOLIC_PATHWAY concepts: - preferred_term: triglyceride biosynthetic process term: id: GO:0019432 label: triglyceride biosynthetic process description: >- ER assembly of triacylglycerol from glycerol-3-phosphate and acyl donors via the Kennedy pathway plus the acyl-CoA-independent PDAT route. - preferred_term: seed oilbody biogenesis term: id: GO:0010344 label: seed oilbody biogenesis context: taxa: - preferred_term: oilseed angiosperms (Arabidopsis and crop oilseeds) cellular_components: - preferred_term: endoplasmic reticulum membrane (Kennedy-pathway enzymes) term: id: GO:0005789 label: endoplasmic reticulum membrane - preferred_term: lipid droplet / oil body (storage organelle) term: id: GO:0005811 label: lipid droplet parts: - order: 1 role: glycerol-3-phosphate acylation to lysophosphatidic acid node: id: gpat_step label: Glycerol-3-phosphate acyltransferase (GPAT) module_type: REACTION annotons: - id: gpat_activity label: Glycerol-3-phosphate O-acyltransferase participant: selector_type: FAMILY family: preferred_term: ER glycerol-3-phosphate acyltransferase (GPAT9) representative_members: - preferred_term: Arabidopsis GPAT9 term: id: UniProtKB:Q8GWG0 label: GPAT9_ARATH function: preferred_term: glycerol-3-phosphate O-acyltransferase activity term: id: GO:0004366 label: glycerol-3-phosphate O-acyltransferase activity substrates: - preferred_term: sn-glycerol 3-phosphate - preferred_term: acyl-CoA products: - preferred_term: 1-acyl-sn-glycerol 3-phosphate (lysophosphatidic acid) - preferred_term: CoA locations: - preferred_term: endoplasmic reticulum membrane term: id: GO:0005789 label: endoplasmic reticulum membrane role_description: >- First committed acylation of the glycerol backbone at sn-1, initiating de novo glycerolipid assembly on the ER. - order: 2 role: lysophosphatidic acid acylation to phosphatidic acid node: id: lpaat_step label: Lysophosphatidic acid acyltransferase (LPAAT) module_type: REACTION annotons: - id: lpaat_activity label: 1-acylglycerol-3-phosphate O-acyltransferase participant: selector_type: FAMILY family: preferred_term: lysophosphatidic acid acyltransferase (LPAT2) representative_members: - preferred_term: Arabidopsis LPAT2 term: id: UniProtKB:Q8LG50 label: LPAT2_ARATH function: preferred_term: 1-acylglycerol-3-phosphate O-acyltransferase activity term: id: GO:0003841 label: 1-acylglycerol-3-phosphate O-acyltransferase activity substrates: - preferred_term: 1-acyl-sn-glycerol 3-phosphate - preferred_term: acyl-CoA products: - preferred_term: 1,2-diacyl-sn-glycerol 3-phosphate (phosphatidic acid) - preferred_term: CoA locations: - preferred_term: endoplasmic reticulum membrane term: id: GO:0005789 label: endoplasmic reticulum membrane role_description: >- sn-2 acylation completing phosphatidic acid, the branch point to both storage (TAG) and membrane (phospholipid) glycerolipids. - order: 3 role: phosphatidic acid dephosphorylation to diacylglycerol node: id: pap_step label: Phosphatidate phosphatase (PAP) module_type: REACTION annotons: - id: pap_activity label: Phosphatidate phosphatase participant: selector_type: FAMILY family: preferred_term: phosphatidic acid phosphatase (PAH) representative_members: - preferred_term: Arabidopsis PAH1 term: id: UniProtKB:Q9SF47 label: PAH1_ARATH function: preferred_term: phosphatidate phosphatase activity term: id: GO:0008195 label: phosphatidate phosphatase activity substrates: - preferred_term: phosphatidic acid products: - preferred_term: 1,2-diacyl-sn-glycerol (DAG) - preferred_term: phosphate locations: - preferred_term: cytosol (amphitropic; recruited to the ER membrane) term: id: GO:0005829 label: cytosol role_description: >- Generates the diacylglycerol acceptor consumed by the final TAG- forming acyltransferases. - order: 4 role: final acyl transfer to diacylglycerol forming triacylglycerol node: id: tag_formation label: Diacylglycerol acylation to TAG module_type: METABOLIC_PATHWAY description: >- The committed, oil-defining step. Plants use two mechanistically distinct and genetically redundant routes to acylate DAG at sn-3. variant_sets: - id: tag_acyl_route label: Acyl-CoA-dependent vs acyl-CoA-independent TAG synthesis axis: acyl donor / enzyme chemistry selection: ONE_OR_MORE variants: - id: dgat_route label: Acyl-CoA-dependent (DGAT1/DGAT2) module_type: REACTION annotons: - id: dgat_activity label: Diacylglycerol O-acyltransferase participant: selector_type: FAMILY family: preferred_term: diacylglycerol acyltransferase (DGAT1/DGAT2) representative_members: - preferred_term: Arabidopsis DGAT1 (TAG1) term: id: UniProtKB:Q9SLD2 label: DGAT1_ARATH - preferred_term: Arabidopsis DGAT2 term: id: UniProtKB:Q9ASU1 label: DGAT2_ARATH - preferred_term: Soybean DGAT1B (GmDGAT1B) term: id: UniProtKB:I1MSF2 label: DAT1B_SOYBN - preferred_term: Soybean DGAT2D (GmDGAT2D) term: id: UniProtKB:K7K424 label: DAT2D_SOYBN ancestral_nodes: - preferred_term: PAINT IBD node PTN000045226 (DGAT1) in PTHR10408 term: id: PANTHER:PTN000045226 label: PTN000045226 description: >- Local PAINT IBD node in PTHR10408 propagating F:GO:0004144 (diacylglycerol O-acyltransferase activity) and P:GO:0019432 (triglyceride biosynthetic process); seeds include the exemplar AT2G19450 (DGAT1) alongside metazoan DGAT1 orthologs, so the node grounds the DGAT1 lineage (DGAT2 is a distinct family, PTHR12317); PAINT date 20200807. evidence: - source_id: GO_REF:0000033 statement: IBD propagation from PAINT node PTN000045226 in PTHR10408. - preferred_term: PAINT IBD node PTN000268127 (DGAT2) in PTHR12317 term: id: PANTHER:PTN000268127 label: PTN000268127 description: >- Local PAINT IBD node in PTHR12317 propagating F:GO:0004144 (diacylglycerol O-acyltransferase activity) and P:GO:0019432 (triglyceride biosynthetic process); seeds include the exemplar AT3G51520 (DGAT2) and soybean DGAT2D (K7K424). DGAT2 (PTHR12317) is non-homologous to DGAT1 (PTHR10408) yet convergently carries the same DGAT activity, so each lineage is grounded on its own node; PAINT date 20250903. evidence: - source_id: GO_REF:0000033 statement: IBD propagation from PAINT node PTN000268127 in PTHR12317. function: preferred_term: diacylglycerol O-acyltransferase activity term: id: GO:0004144 label: diacylglycerol O-acyltransferase activity substrates: - preferred_term: 1,2-diacyl-sn-glycerol - preferred_term: acyl-CoA products: - preferred_term: triacylglycerol - preferred_term: CoA locations: - preferred_term: endoplasmic reticulum membrane term: id: GO:0005789 label: endoplasmic reticulum membrane role_description: >- Uses acyl-CoA as the sn-3 acyl donor; DGAT1 carries most bulk TAG flux and is the primary seed-oil-yield engineering target. - id: pdat_route label: Acyl-CoA-independent (PDAT) module_type: REACTION annotons: - id: pdat_activity label: Phospholipid:diacylglycerol acyltransferase participant: selector_type: FAMILY family: preferred_term: phospholipid:diacylglycerol acyltransferase (PDAT) representative_members: - preferred_term: Arabidopsis PDAT1 term: id: UniProtKB:Q9FNA9 label: PDAT1_ARATH function: preferred_term: phospholipid:diacylglycerol acyltransferase activity term: id: GO:0046027 label: phospholipid:diacylglycerol acyltransferase activity substrates: - preferred_term: phospholipid (e.g. phosphatidylcholine) - preferred_term: 1,2-diacyl-sn-glycerol products: - preferred_term: triacylglycerol - preferred_term: lysophospholipid locations: - preferred_term: endoplasmic reticulum membrane term: id: GO:0005789 label: endoplasmic reticulum membrane role_description: >- Transfers an acyl group from the sn-2 of a phospholipid to DAG without acyl-CoA; redundant with DGAT1 and jointly essential for seed/pollen oil. - order: 5 role: oil-body biogenesis and oleosin stabilization node: id: oil_body_packaging label: Oil-body (lipid droplet) biogenesis and oleosin coating module_type: CELLULAR_COMPONENT description: >- TAG accumulates between the ER bilayer leaflets and buds into cytosolic oil bodies bounded by a phospholipid monolayer studded with oleosins, which set droplet size and prevent coalescence - critical for desiccation tolerance and for oil recovery from the seed. annotons: - id: oleosin_stabilization label: Oleosin oil-body structural coating participant: selector_type: FAMILY family: preferred_term: seed oleosin representative_members: - preferred_term: Arabidopsis OLEO2 (oleosin 21.2 kDa) term: id: UniProtKB:Q39165 label: OLEO2_ARATH function: preferred_term: oil-body structural constituent description: >- Oleosins are amphipathic structural proteins embedding in the oil-body monolayer; they act structurally rather than catalytically, so no GO molecular-function term is asserted here. processes: - preferred_term: seed oilbody biogenesis term: id: GO:0010344 label: seed oilbody biogenesis locations: - preferred_term: lipid droplet / oil body term: id: GO:0005811 label: lipid droplet - preferred_term: monolayer-surrounded lipid storage body term: id: GO:0012511 label: monolayer-surrounded lipid storage body role_description: >- Coats the oil body, controlling droplet size and stability; oleosin dosage tunes oil-body number and total oil packaging capacity. connections: - source: gpat_step target: lpaat_step connection_type: PRECEDES chaining_status: VERIFIED chaining_note: >- GPAT produces lysophosphatidic acid, the acceptor acylated by LPAAT to phosphatidic acid. - source: lpaat_step target: pap_step connection_type: PRECEDES chaining_status: VERIFIED chaining_note: >- LPAAT produces phosphatidic acid, which PAP dephosphorylates to diacylglycerol. - source: pap_step target: tag_formation connection_type: PROVIDES_INPUT_FOR description: PAP-derived diacylglycerol is the acceptor for the final TAG-forming step. - source: tag_formation target: oil_body_packaging connection_type: PROVIDES_INPUT_FOR description: Newly synthesized TAG accumulates in and buds into oleosin-coated oil bodies.