Bacterial de novo phosphatidic acid synthesis (PlsX/PlsY and PlsB routes)

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.

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.