id: MODULE:bacterial_phosphatidic_acid_synthesis title: Bacterial de novo phosphatidic acid synthesis (PlsX/PlsY and PlsB routes) description: >- A reusable bacterial module for de novo synthesis of phosphatidic acid, the branch-point precursor of all membrane glycerophospholipids, from sn-glycerol 3-phosphate and the activated fatty acids made by type II fatty acid synthase. The module has two steps. The first acylation esterifies a fatty acyl group to the sn-1 position of sn-glycerol 3-phosphate to give 1-acyl-sn-glycerol 3-phosphate (lysophosphatidic acid), and is implemented by either of two routes: the ubiquitous acyl-phosphate route, in which PlsX converts acyl-[ACP] into acyl-phosphate and the polytopic membrane protein PlsY transfers that acyl group to glycerol 3-phosphate, or the PlsB route, in which a single peripheral membrane acyltransferase acylates glycerol 3-phosphate directly from acyl-CoA or acyl-[ACP]. The second acylation, by PlsC of the AGPAT/LPAAT family, adds a fatty acyl group to the sn-2 position of lysophosphatidic acid to give phosphatidic acid, and is common to both routes. status: DRAFT scope: CONCRETE evidence: - source_id: GO:0006654 title: phosphatidic acid biosynthetic process statement: >- GO:0006654 captures biosynthesis of phosphatidic acid, the product at which this module ends. - source_id: RHEA:42292 title: acyl-[acyl-carrier-protein]--phosphate acyltransferase reaction statement: >- Rhea 42292 defines reversible formation of an acyl phosphate from a fatty acyl-[ACP] and phosphate, the PlsX reaction (EC 2.3.1.274). - source_id: RHEA:34075 title: acyl-phosphate--glycerol-3-phosphate acyltransferase reaction statement: >- Rhea 34075 defines acyl transfer from an acyl phosphate to sn-glycerol 3-phosphate to give 1-acyl-sn-glycero-3-phosphate and phosphate, the PlsY reaction (EC 2.3.1.275). - source_id: RHEA:15325 title: glycerol-3-phosphate O-acyltransferase reaction (acyl-CoA donor) statement: >- Rhea 15325 defines acyl transfer from an acyl-CoA to sn-glycerol 3-phosphate to give 1-acyl-sn-glycero-3-phosphate and CoA, the PlsB reaction (EC 2.3.1.15). - source_id: RHEA:42300 title: >- glycerol-3-phosphate O-acyltransferase reaction (acyl-[ACP] donor) statement: >- Rhea 42300 defines the same sn-1 acylation of sn-glycerol 3-phosphate with a fatty acyl-[ACP] donor, which E. coli PlsB also uses. - source_id: RHEA:42296 title: >- 1-acyl-sn-glycerol-3-phosphate acyltransferase reaction (acyl-[ACP] donor) statement: >- Rhea 42296 defines acyl transfer from a fatty acyl-[ACP] to a 1-acyl-sn-glycero-3-phosphate to give a 1,2-diacyl-sn-glycero-3-phosphate and holo-[ACP]; this is the donor form used by B. subtilis PlsC, which does not use acyl-CoA. - source_id: RHEA:19709 title: >- 1-acyl-sn-glycerol-3-phosphate acyltransferase reaction (acyl-CoA donor) statement: >- Rhea 19709 defines the same sn-2 acylation with an acyl-CoA donor (EC 2.3.1.51); E. coli PlsC uses either donor. - source_id: PMID:42286214 title: >- Bacterial lipid synthesizing enzymes PlsY and PlsC utilize both stereo-forms of glycerol-phosphate. statement: >- The introduction and Fig. 1A of this paper give the route structure modelled here: PlsX feeds acyl-phosphate to PlsY in the ubiquitous route, PlsB is an alternative first acyltransferase largely restricted to proteobacteria and actinobacteria, and PlsC performs the sn-2 acylation in both routes. supporting_text: >- The PlsX/PlsY system is ubiquitous in the majority of bacterial taxa, while PlsB is largely restricted to proteobacteria and actinobacteria. - source_id: PMID:42286214 title: >- Bacterial lipid synthesizing enzymes PlsY and PlsC utilize both stereo-forms of glycerol-phosphate. statement: >- PlsX activation of acyl-[ACP] to acyl-phosphate is a prerequisite of the PlsY route, which is why PlsX is modelled inside that route rather than as a step shared with the PlsB route. supporting_text: >- For this, acyl-ACP, first has to be converted by the phosphate acyltransferase PlsX into acyl-phosphate (acyl-Pi), which in turn can be utilized by PlsY. - source_id: PMID:42286214 title: >- Bacterial lipid synthesizing enzymes PlsY and PlsC utilize both stereo-forms of glycerol-phosphate. statement: >- Xanthomonadales carry only PlsB and PlsC, which is the case that requires the first acylation to be a route-level alternative rather than a single obligatory PlsX/PlsY step. supporting_text: >- Bacteria belonging to the phylum Xanthomonadales only contain the PlsB and PlsC enzymes for phospholipid biosynthesis - source_id: PMID:17645809 title: >- Involvement of the YneS/YgiH and PlsX proteins in phospholipid biosynthesis in both Bacillus subtilis and Escherichia coli. statement: >- In vivo genetics establish that the PlsX/PlsY route is sufficient and essential in bacteria without PlsB, and that E. coli runs both routes, with PlsB dominant; this is why the route variant set allows one or more branches rather than exactly one. supporting_text: >- the PlsX/Y pathway is essential for the growth of bacteria lacking plsB - source_id: PMID:17645809 title: >- Involvement of the YneS/YgiH and PlsX proteins in phospholipid biosynthesis in both Bacillus subtilis and Escherichia coli. statement: >- Both first-acylation routes operate in E. coli, with PlsB carrying most of the flux. supporting_text: >- although PlsB plays the principal role in 1-acyl-G3P synthesis, PlsX and YgiH are also important for optimal E. coli growth - source_id: PMID:17557823 title: Coupling of fatty acid and phospholipid synthesis in Bacillus subtilis. statement: >- B. subtilis PlsC uses acyl-[ACP] and not acyl-CoA, so the acyl-[ACP] reaction (Rhea 42296) is the donor form modelled for the second acylation in the PlsX/PlsY-only case. supporting_text: whereas PlsC used only acyl-ACP as an acyl donor - source_id: file:BACSU/plsY/plsY-ai-review.yaml title: BACSU plsY gene review statement: >- The completed review of Q45064 accepts GO:0043772 as the core molecular function, places it at the plasma membrane, and refines the generic phospholipid process rows to GO:0006654 phosphatidic acid biosynthetic process; the module uses exactly those assertions. - source_id: file:BACSU/plsC/plsC-ai-review.yaml title: BACSU plsC gene review statement: >- The completed review of O07584 accepts GO:0003841 as the core molecular function with GO:0006654 as the process and the plasma membrane as the location, and notes that GO:0003841 and its parents are written with an acyl-CoA donor although bacterial PlsC uses acyl-[ACP]. notes: >- Boundary. The module begins with sn-glycerol 3-phosphate and the activated fatty acids delivered by type II fatty acid synthase, and ends at phosphatidic acid. Supply of the glycerol-phosphate backbone (GpsA/GlpD/GlpK, and the glycerol-1-phosphate dehydrogenase AraM/EgsA) and supply of acyl-[ACP] or acyl-CoA (modules type_ii_fatty_acid_synthesis, fatty_acid_elongation_cycle, bacterial_unsaturated_fatty_acid_biosynthesis) are upstream and out of scope. Downstream chemistry is deliberately not duplicated: activation of phosphatidic acid to CDP-diacylglycerol and the head-group transfers are covered by cdp_dag_phospholipid_synthesis, the bacterial PG and cardiolipin branch by bacterial_phosphatidylglycerol_cardiolipin_biosynthesis, and the bacterial PE branch by bacterial_phosphatidylethanolamine_biosynthesis. Those three modules all start at CDP-diacylglycerol or later, so phosphatidic acid is the clean join, and bacterial CdsA (phosphatidate cytidylyltransferase) is the one reaction that currently sits between this module and them, modelled in neither; it is noted here as a curation gap rather than pulled inside the boundary. Acyl-chain remodeling, phosphatidic acid turnover by phosphatases and lipases, and regulation (FapR control of plsX, the PlsX-PlsY coupling that ties phospholipid to fatty acid synthesis) are also outside the boundary. Structure. The user-proposed three-step layout (PlsX, then first acylation, then PlsC) was tested and adjusted: PlsX is required only by the PlsY route, because Xanthomonadales run the pathway with PlsB and PlsC alone (PMID:42286214). Keeping PlsX as a top-level obligatory step would therefore make the module unsatisfiable for those taxa. PlsX is instead modelled as the first of two ordered steps inside the PlsX/PlsY route variant, so the module has two top-level parts (first acylation, second acylation), the first of which carries a ROUTE variant set whose branches are the two-reaction acyl-phosphate route and the one-reaction PlsB route. The variant set allows one or more branches because E. coli has both. Stereochemistry. Rieche et al. (PMID:42286214) show that purified B. subtilis and E. coli PlsY acylate sn-glycerol 1-phosphate as well as sn-glycerol 3-phosphate, and that PlsC acylates both lysophosphatidic acid enantiomers, while PlsB is strictly specific for sn-glycerol 3-phosphate. The modelled reaction chemistry nevertheless stays G3P/LPA/PA throughout, mirroring the judgement already recorded in the BACSU plsY and plsC reviews: in a membrane PlsY clearly prefers G3P, no kinetic constants exist, the (S)-LPA result is confounded by substrate supply in a coupled assay, the in vivo source of glycerol 1-phosphate is unidentified, and the heterochiral-lipid report that motivates the inference (PMID:35767906) is a single unreplicated abstract. Under the in-vitro-activity tiers of projects/ENZYME_SPECIFICITY.md this is real in vitro activity of unestablished physiological relevance, so it is recorded as a module knowledge gap and not as a modelled part, variant, substrate or asserted function. GO has no term for either G1P reaction; the requests live in the plsY and plsC reviews' proposed_new_terms and are not restated here. The stereospecificity difference does, however, bear on the route variants: only the PlsY branch has the capability at all, which is recorded in that branch's description and in the gap. Grounding. Every PANTHER family label is PANTHER's own name, taken verbatim from interpro/panther/panther.obo. Only one PAINT ancestral node is asserted per annoton where the node's own IBD is for the annoton's function: PTN000046632 for GO:0003841 in PTHR10434 (confirmed in interpro/panther/PTHR10434/PTHR10434-paint.tsv and in the O07584 GOA WITH/FROM) and PTN000285870 for GO:0004366 in PTHR12563 (confirmed in interpro/panther/PTHR12563/PTHR12563-paint.tsv, seeded by P0A7A7 at taxon:1236). No node is asserted for PlsX or PlsY: PTHR30100 and PTHR30309 have no cached PAINT file, and the only PlsY node available from GOA (PTN001250899) carries an IBD for plasma membrane, not for GO:0043772, so using it as the ancestral node of the acyltransferase annoton would overstate what PAINT asserts. BACSU plsX, ECOLI plsX, ECOLI plsY, ECOLI plsC and ECOLI plsB have no gene review in this repository yet, which the QC panel reports as a coverage notice. module: id: bacterial_phosphatidic_acid_synthesis label: Bacterial de novo phosphatidic acid synthesis module_type: METABOLIC_PATHWAY concepts: - preferred_term: phosphatidic acid biosynthetic process term: id: GO:0006654 label: phosphatidic acid biosynthetic process description: >- Two successive acylations of sn-glycerol 3-phosphate that produce phosphatidic acid, the common precursor of bacterial membrane glycerophospholipids. context: taxa: - preferred_term: bacteria term: id: NCBITaxon:2 label: Bacteria description: >- The module represents the general bacterial route. The PlsX/PlsY implementation is near-universal; the PlsB implementation is largely confined to proteobacteria and actinobacteria. evidence: - source_id: PMID:42286214 title: >- Bacterial lipid synthesizing enzymes PlsY and PlsC utilize both stereo-forms of glycerol-phosphate. statement: >- Fig. 1A states the taxonomic distribution of the two first-acylation routes. supporting_text: >- The PlsX/PlsY system is ubiquitous in the majority of bacterial taxa, while PlsB is largely restricted to proteobacteria and actinobacteria. parts: - order: 1 role: first acylation of glycerol 3-phosphate node: id: first_acylation_to_lysophosphatidic_acid label: sn-1 acylation of sn-glycerol 3-phosphate to lysophosphatidic acid module_type: BIOLOGICAL_PROCESS description: >- Esterification of a fatty acyl group to the sn-1 position of sn-glycerol 3-phosphate, giving 1-acyl-sn-glycero-3-phosphate. This is the committing step of membrane phospholipid synthesis and is implemented by one of two routes that differ in the acyl donor and in the number of enzymes required. variant_sets: - id: first_acylation_route label: Route to lysophosphatidic acid axis: acyl donor chemistry and enzyme complement of the first acylation variant_kind: ROUTE selection: ONE_OR_MORE notes: >- ONE_OR_MORE rather than EXACTLY_ONE because E. coli runs both routes, with PlsB carrying most of the flux and the PlsX/PlsY pair still contributing to optimal growth. evidence: - source_id: PMID:17645809 title: >- Involvement of the YneS/YgiH and PlsX proteins in phospholipid biosynthesis in both Bacillus subtilis and Escherichia coli. statement: >- Both routes are present and functional in E. coli, while the PlsX/PlsY route alone suffices in bacteria lacking plsB. supporting_text: >- although PlsB plays the principal role in 1-acyl-G3P synthesis, PlsX and YgiH are also important for optimal E. coli growth variants: - id: acyl_phosphate_plsx_plsy_route label: Acyl-phosphate route (PlsX then PlsY) module_type: METABOLIC_PATHWAY description: >- The near-universal bacterial route. PlsX first transfers the acyl group of acyl-[ACP] to inorganic phosphate, making the soluble high-energy donor acyl-phosphate; the polytopic membrane protein PlsY then transfers that acyl group to sn-glycerol 3-phosphate. PlsY uses neither acyl-CoA nor acyl-[ACP], so the two reactions are obligatorily coupled. This is also the only branch for which use of the non-canonical sn-glycerol 1-phosphate backbone has been observed in vitro; see the module knowledge gaps. parts: - order: 1 role: acyl donor activation node: id: plsx_acyl_phosphate_formation label: PlsX-dependent acyl-phosphate formation module_type: REACTION annotons: - id: plsx_activity label: PlsX phosphate acyltransferase activity participant: selector_type: FAMILY family: preferred_term: PlsX phosphate acyltransferase family term: id: PANTHER:PTHR30100 label: FATTY ACID/PHOSPHOLIPID SYNTHESIS PROTEIN PLSX description: >- The PlsX family (Pfam PF02504, InterPro IPR003664/IPR012281, HAMAP MF_00019). No PAINT file is cached for this family, so no ancestral node is asserted. representative_members: - preferred_term: PlsX (Bacillus subtilis 168) term: id: UniProtKB:P71018 label: Phosphate acyltransferase description: >- Reviewed exemplar from a species whose only first-acylation route is PlsX/PlsY. - preferred_term: PlsX (Escherichia coli K-12) term: id: UniProtKB:P27247 label: Phosphate acyltransferase description: >- Reviewed exemplar from a species that also has PlsB; its GO:0043811 row is IMP from EcoCyc. function: preferred_term: >- phosphate:acyl-[acyl carrier protein] acyltransferase activity term: id: GO:0043811 label: >- phosphate:acyl-[acyl carrier protein] acyltransferase activity description: >- Reversible formation of acyl-phosphate from acyl-[ACP] and inorganic phosphate. The enzyme uses acyl-[ACP] and not acyl-CoA. substrates: - preferred_term: fatty acyl-[ACP] - preferred_term: phosphate products: - preferred_term: acyl phosphate - preferred_term: holo-[ACP] evidence: - source_id: RHEA:42292 title: >- acyl-[acyl-carrier-protein]--phosphate acyltransferase reaction statement: >- Rhea 42292, EC 2.3.1.274, is the reaction assigned to both PlsX exemplars by HAMAP rule MF_00019. - source_id: PMID:42286214 title: >- Bacterial lipid synthesizing enzymes PlsY and PlsC utilize both stereo-forms of glycerol-phosphate. statement: >- PlsX activation of acyl-[ACP] is stated as the prerequisite of the PlsY reaction. supporting_text: >- For this, acyl-ACP, first has to be converted by the phosphate acyltransferase PlsX into acyl-phosphate (acyl-Pi), which in turn can be utilized by PlsY. processes: - preferred_term: phosphatidic acid biosynthetic process term: id: GO:0006654 label: phosphatidic acid biosynthetic process description: >- PlsX makes the dedicated donor consumed by PlsY in this route. Its GOA rows currently stop at the generic phospholipid terms (GO:0006644, GO:0008654) and no plsX gene review exists yet, so this is the module's own refinement, parallel to the refinement accepted in the BACSU plsY review. locations: - preferred_term: cytoplasm term: id: GO:0005737 label: cytoplasm description: >- UniProt places PlsX in the cytoplasm and notes probable membrane association through PlsY; no transmembrane segment is predicted. role_description: >- Converts acyl-[ACP] from fatty acid synthesis into the acyl-phosphate donor that PlsY requires. - order: 2 role: glycerol-3-phosphate acylation node: id: plsy_g3p_acylation label: PlsY-dependent acylation of sn-glycerol 3-phosphate module_type: REACTION annotons: - id: plsy_activity label: >- PlsY acyl-phosphate glycerol-3-phosphate acyltransferase activity participant: selector_type: FAMILY family: preferred_term: PlsY glycerol-phosphate acyltransferase family term: id: PANTHER:PTHR30309 label: INNER MEMBRANE PROTEIN YGIH description: >- The PlsY family (Pfam PF02660, InterPro IPR003811, HAMAP MF_01043); PANTHER names it after the E. coli locus ygiH, the original name of plsY. No PAINT file is cached for this family, and the only PlsY PAINT node reachable from GOA (PTN001250899) carries an IBD for plasma membrane rather than for GO:0043772, so no ancestral node is asserted here. representative_members: - preferred_term: PlsY (Bacillus subtilis 168) term: id: UniProtKB:Q45064 label: Glycerol-3-phosphate acyltransferase description: >- Sole GPAT of B. subtilis; the completed review accepts GO:0043772 as its core molecular function. - preferred_term: PlsY (Escherichia coli K-12) term: id: UniProtKB:P60782 label: Probable glycerol-3-phosphate acyltransferase description: >- The E. coli member, which operates alongside PlsB; UniProt keeps its donor assignment partly as Probable. function: preferred_term: >- acyl-phosphate glycerol-3-phosphate acyltransferase activity term: id: GO:0043772 label: >- acyl-phosphate glycerol-3-phosphate acyltransferase activity description: >- Transfer of an acyl group from acyl-phosphate to the sn-1 position of sn-glycerol 3-phosphate, releasing phosphate. B. subtilis PlsY uses acyl-phosphate and neither acyl-CoA nor acyl-[ACP]. substrates: - preferred_term: acyl phosphate - preferred_term: sn-glycerol 3-phosphate products: - preferred_term: 1-acyl-sn-glycero-3-phosphate - preferred_term: phosphate evidence: - source_id: RHEA:34075 title: >- acyl-phosphate--glycerol-3-phosphate acyltransferase reaction statement: >- Rhea 34075, EC 2.3.1.275, is the reaction assigned to Q45064. - source_id: file:BACSU/plsY/plsY-ai-review.yaml title: BACSU plsY gene review statement: >- The completed review accepts GO:0043772 as the core molecular function of Q45064 on direct evidence from B. subtilis membranes. processes: - preferred_term: phosphatidic acid biosynthetic process term: id: GO:0006654 label: phosphatidic acid biosynthetic process locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane description: >- Polytopic integral protein of the cytoplasmic (inner) membrane; the acyl-phosphate-dependent activity is in the membrane fraction and is lost in a plsY deletion. role_description: >- Performs the committing sn-1 acylation and supplies lysophosphatidic acid to PlsC. connections: - source: plsx_acyl_phosphate_formation target: plsy_g3p_acylation connection_type: PROVIDES_INPUT_FOR description: >- PlsX supplies the acyl-phosphate donor that PlsY requires; PlsY cannot use acyl-[ACP] or acyl-CoA. chaining_status: VERIFIED chaining_note: >- The acyl phosphate product of Rhea 42292 is the acyl donor substrate of Rhea 34075. The intermediate carries no CoA, so the automated CoA-continuity matcher cannot check it. - id: plsb_route label: PlsB route (direct acylation from acyl-CoA or acyl-[ACP]) module_type: REACTION description: >- A single peripheral membrane acyltransferase of the GPAT/DAPAT family acylates sn-glycerol 3-phosphate directly, using either acyl-CoA or acyl-[ACP], so no acyl-phosphate intermediate and no PlsX are needed. The route is largely confined to proteobacteria and actinobacteria; in E. coli it coexists with PlsX/PlsY and carries most of the flux, while Xanthomonadales have only PlsB and PlsC. Unlike PlsY, PlsB is strictly specific for sn-glycerol 3-phosphate. annotons: - id: plsb_activity label: PlsB glycerol-3-phosphate O-acyltransferase activity participant: selector_type: FAMILY family: preferred_term: >- PlsB-type glycerol-3-phosphate acyltransferase lineage of the GPAT/DAPAT family term: id: PANTHER:PTHR12563 label: GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE description: >- PTHR12563 is heterogeneous: besides bacterial PlsB it contains mitochondrial GPAT1/GPAT2 and dihydroxyacetone-phosphate acyltransferases, and the cached family review records GO:0004366 as UNRESOLVED at family scope for that reason. The required ancestral node restricts this annoton to the PlsB lineage. representative_members: - preferred_term: PlsB (Escherichia coli K-12) term: id: UniProtKB:P0A7A7 label: Glycerol-3-phosphate acyltransferase description: >- The characterized bacterial exemplar, with measured kinetics, inner-membrane peripheral localization and EC 2.3.1.15. ancestral_nodes: - preferred_term: PlsB PAINT node PTN000285870 term: id: PANTHER:PTN000285870 label: PTN000285870 description: >- The PTHR12563 node whose IBD for GO:0004366 is seeded by E. coli PlsB (P0A7A7) at taxon:1236 (Gammaproteobacteria). The node's taxon is narrower than the proteobacteria-plus-actinobacteria distribution reported for PlsB, so the node grounds the gammaproteobacterial case and is not evidence for actinobacterial PlsB. evidence: - source_id: GO_REF:0000033 statement: >- PAINT curator propagation (IBD) places GO:0004366 at this node. - source_id: file:interpro/panther/PTHR12563/PTHR12563-paint.tsv statement: >- The cached PAINT table lists PTHR12563 PTN000285870 GO:0004366 F IBD with seed UniProtKB:P0A7A7 and taxon:1236. function: preferred_term: glycerol-3-phosphate O-acyltransferase activity term: id: GO:0004366 label: glycerol-3-phosphate O-acyltransferase activity description: >- Transfer of an acyl group to the sn-1 position of sn-glycerol 3-phosphate. GO:0004366 and its Rhea 15325 cross-reference are written with an acyl-CoA donor; E. coli PlsB also uses acyl-[ACP] (Rhea 42300), so the term under-describes the donor range of the bacterial enzyme in the same way that GO:0003841 does for PlsC. substrates: - preferred_term: sn-glycerol 3-phosphate - preferred_term: acyl-CoA or fatty acyl-[ACP] products: - preferred_term: 1-acyl-sn-glycero-3-phosphate - preferred_term: CoA or holo-[ACP] evidence: - source_id: RHEA:15325 title: >- glycerol-3-phosphate O-acyltransferase reaction (acyl-CoA donor) statement: >- Rhea 15325, EC 2.3.1.15, is the reaction assigned to P0A7A7 with experimental evidence. - source_id: PMID:42286214 title: >- Bacterial lipid synthesizing enzymes PlsY and PlsC utilize both stereo-forms of glycerol-phosphate. statement: >- PlsB accepts either activated-fatty-acid donor directly, without an acyl-phosphate intermediate. supporting_text: >- This enzyme can directly utilize acyl-CoA and acyl-ACP. processes: - preferred_term: phosphatidic acid biosynthetic process term: id: GO:0006654 label: phosphatidic acid biosynthetic process locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane description: >- Peripheral protein on the cytoplasmic face of the inner membrane, in a complex with ACP, YbgC and PssA. role_description: >- Performs the sn-1 acylation in one step and supplies lysophosphatidic acid to PlsC. - order: 2 role: second acylation to phosphatidic acid node: id: plsc_phosphatidic_acid_formation label: PlsC-dependent formation of phosphatidic acid module_type: REACTION description: >- Transfer of a fatty acyl group to the sn-2 position of 1-acyl-sn-glycero-3-phosphate, giving phosphatidic acid. This step is shared by both first-acylation routes and is the end of the module. annotons: - id: plsc_activity label: >- PlsC 1-acylglycerol-3-phosphate O-acyltransferase activity participant: selector_type: FAMILY family: preferred_term: PlsC/AGPAT lysophosphatidic acid acyltransferase family term: id: PANTHER:PTHR10434 label: 1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE description: >- The LPAAT/AGPAT family (Pfam PF01553, InterPro IPR004552), carrying the HXXXXD acyltransferase motif. It spans bacterial PlsC and the eukaryotic AGPATs, and the ancestral node below is the one whose IBD covers the shared LPAAT activity. representative_members: - preferred_term: PlsC (Bacillus subtilis 168) term: id: UniProtKB:O07584 label: 1-acyl-sn-glycerol-3-phosphate acyltransferase description: >- The only PlsC/AGPAT-family protein of B. subtilis and indispensable; it uses acyl-[ACP] and not acyl-CoA. - preferred_term: PlsC (Escherichia coli K-12) term: id: UniProtKB:P26647 label: 1-acyl-sn-glycerol-3-phosphate acyltransferase description: >- Uses either acyl-CoA or acyl-[ACP]; its GO:0003841 row is IDA from EcoCyc and it seeds the PAINT node below. ancestral_nodes: - preferred_term: LPAAT PAINT node PTN000046632 term: id: PANTHER:PTN000046632 label: PTN000046632 description: >- The PTHR10434 node carrying the IBD for GO:0003841, seeded by plant, mouse, yeast and human AGPATs together with E. coli PlsC (P26647); B. subtilis PlsC receives the activity as an IBA from it. evidence: - source_id: GO_REF:0000033 statement: >- PAINT curator propagation (IBD) places GO:0003841 and GO:0006654 at this node. - source_id: file:interpro/panther/PTHR10434/PTHR10434-paint.tsv statement: >- The cached PAINT table lists PTHR10434 PTN000046632 GO:0003841 F IBD with UniProtKB:P26647 among the seeds. function: preferred_term: 1-acylglycerol-3-phosphate O-acyltransferase activity term: id: GO:0003841 label: 1-acylglycerol-3-phosphate O-acyltransferase activity description: >- Acylation of the sn-2 position of 1-acyl-sn-glycero-3-phosphate to give 1,2-diacyl-sn-glycero-3-phosphate. GO:0003841 and both its parents are written with an acyl-CoA donor, whereas B. subtilis PlsC uses acyl-[ACP] only (Rhea 42296) and E. coli PlsC uses either; the donor-specific term request is recorded in the BACSU plsC review. substrates: - preferred_term: 1-acyl-sn-glycero-3-phosphate - preferred_term: fatty acyl-[ACP] or acyl-CoA products: - preferred_term: 1,2-diacyl-sn-glycero-3-phosphate (phosphatidic acid) - preferred_term: holo-[ACP] or CoA evidence: - source_id: RHEA:42296 title: >- 1-acyl-sn-glycerol-3-phosphate acyltransferase reaction (acyl-[ACP] donor) statement: >- Rhea 42296 is the reaction assigned to O07584 and is one of the two assigned to P26647. - source_id: PMID:17557823 title: >- Coupling of fatty acid and phospholipid synthesis in Bacillus subtilis. statement: >- B. subtilis PlsC is acyl-[ACP]-dependent. supporting_text: whereas PlsC used only acyl-ACP as an acyl donor - source_id: file:BACSU/plsC/plsC-ai-review.yaml title: BACSU plsC gene review statement: >- The completed review accepts GO:0003841 as the core molecular function of O07584, with GO:0006654 as the process and the plasma membrane as the location. processes: - preferred_term: phosphatidic acid biosynthetic process term: id: GO:0006654 label: phosphatidic acid biosynthetic process locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane description: >- Peripheral protein of the cytoplasmic (inner) membrane; in B. subtilis it is concentrated in the septal membrane. role_description: >- Completes phosphatidic acid synthesis and hands the product to the CDP-diacylglycerol and head-group modules. connections: - source: first_acylation_to_lysophosphatidic_acid target: plsc_phosphatidic_acid_formation connection_type: PROVIDES_INPUT_FOR description: >- Either first-acylation route supplies 1-acyl-sn-glycero-3-phosphate to PlsC, which is why the second acylation sits above the route variant set rather than inside it. chaining_status: VERIFIED chaining_note: >- The 1-acyl-sn-glycero-3-phosphate product of Rhea 34075, 15325 and 42300 is the acceptor substrate of Rhea 42296 and 19709. The shared intermediate carries no CoA, so the automated CoA-continuity matcher cannot check this link. knowledge_gaps: - gap_statement: >- Whether the first acylation of this module ever uses sn-glycerol 1-phosphate in a living bacterium, and so whether the route has a second, stereochemically distinct product, is unknown. boundary: >- Established: purified B. subtilis and E. coli PlsY acylate sn-glycerol 1-phosphate as well as sn-glycerol 3-phosphate in detergent with only minor differences in product levels, PlsC converts both lysophosphatidic acid enantiomers into phosphatidic acid in a coupled liposome system, and PlsB is strictly specific for sn-glycerol 3-phosphate; separately, a minor glycerol 1-phosphate-backbone phosphatidylglycerol fraction has been reported in B. subtilis, whose only GPAT is PlsY. Unknown: whether PlsY makes that lipid in vivo, what supplies glycerol 1-phosphate, and the kinetic preference of either enzyme, since reconstituted PlsY clearly prefers glycerol 3-phosphate and the (S)-lysophosphatidic acid result is confounded by that substrate's lower concentration in a coupled assay. The module therefore models G3P chemistry only. gap_kind: - BIOLOGY dark_aspect: RESIDUAL_SUBGAP status: OPEN significance: >- This is the bacterial half of the lipid divide (projects/LIPID_DIVIDE.md). If PlsY acylates glycerol 1-phosphate in vivo, one ordinary bacterial acyltransferase accounts for heterochiral membranes, the capability is confined to the PlsY branch of the route variant set, and GO has no molecular function term for either the PlsY or the PlsC reaction on the S enantiomer. The term requests are held in the BACSU plsY and plsC reviews rather than asserted here. resolution: >- Determine kinetic constants of reconstituted PlsY for both glycerol-phosphate enantiomers and of reconstituted PlsC on chemically synthesised (R)- and (S)-lysophosphatidic acid supplied at equal concentrations, uncoupled from PlsY; then test in vivo whether (S)-backbone lipid depends on PlsY, by chiral lipidomics of an araM (egsA) deletion and of PlsY-depleted cells complemented with the strictly G3P-specific E. coli PlsB. provenance: - reference_id: PMID:42286214 supporting_text: >- whereas the GPAT PlsB is strictly stereoselective towards G3P reference_section_type: INTRODUCTION - reference_id: PMID:42286214 supporting_text: >- These data demonstrate that the GPAT PlsY is the key enzyme responsible for the backbone heterochirality observed in bacterial phospholipids. reference_section_type: INTRODUCTION - reference_id: PMID:42286214 supporting_text: >- However, the levels of (R)-LPA (containing a G3P lipid backbone) were significantly higher compared to the levels of (S)-LPA, a difference that was not observed for the enzyme in detergent (Fig. reference_section_type: RESULTS - reference_id: PMID:35767906 supporting_text: >- By using chiral chromatography, the presence of both enantiomers in the glycerol backbone of some molecular species of PG was revealed. reference_section_type: ABSTRACT full_text_unavailable: true - gap_statement: >- Whether PlsX and PlsY form a physical complex that channels acyl-phosphate, rather than releasing it into the cytoplasm, is not established. boundary: >- Acyl-phosphate is a reactive intermediate and UniProt records the PlsX-PlsY interaction only as probable, inferred from the HAMAP rule and from the loss of membrane-associated activity in the absence of either protein. No purified reconstitution or structure of a PlsX-PlsY assembly exists, and PlsX itself has no cached PAINT family data. gap_kind: - BIOLOGY dark_aspect: CC_DARK status: OPEN significance: >- If the two enzymes are an obligate assembly, the acyl-phosphate route is one annoton with a protein-complex participant rather than the two ordered reactions modelled here, and the step is also the point at which phospholipid synthesis is coupled to fatty acid synthesis. resolution: >- Test for a PlsX-PlsY complex by co-purification from native membranes and by crosslinking, and measure whether free acyl-phosphate accumulates or is channelled in a reconstituted system containing both proteins. provenance: - reference_id: PMID:17645809 supporting_text: >- pneumoniae PlsY, YneS, is required for G3P acyltransferase activity, together with PlsX. reference_section_type: DISCUSSION