yxcA encodes the single-chain anaerobic-type plasmalogen synthase PlsA of Lactococcus lactis. The 1436-residue cytoplasmic protein fuses all four modules of the PlsA/PlsR system first defined in Clostridium perfringens: two BadF/BadG/BcrA/BcrD-type ATPase activation domains (Act1, Act2), a DUF2229 reduction/dehydration domain (Red1) and a C-terminal PlsR-like domain (Red2). It belongs to the benzoyl-CoA reductase / 2-hydroxyacyl-CoA dehydratase (BCR/HAD) radical enzyme family. PlsA converts diacyl glycerophospholipids into plasmalogens (1-alk-1'-enyl-2-acyl lipids) by reducing the sn-1 ester bond, rather than by the oxygen-dependent desaturation of an ether used in aerobes. By analogy with the BCR/HAD family, the activation domains are thought to couple ATP hydrolysis to electron transfer through iron-sulfur clusters, making the difficult one-electron ester reduction possible. A Lactococcus cremoris ortholog (96.6% identical) confers plasmalogen synthesis on Escherichia coli, and it does so even in air, unlike the oxygen-sensitive PlsA proteins of other lactic acid bacteria and clostridia. The ProtNLM-derived name "2-hydroxyglutaryl-CoA dehydratase" and the eggNOG name hgdC reflect family membership only. The protein is not a 2-hydroxyglutaryl-CoA dehydratase or its activator.
Definition: Catalysis of the reduction of the sn-1 acyl ester of a 1,2-diacyl-sn-glycero-3-phospholipid to a 1-(1Z-alkenyl) ether, forming the corresponding 1-(1Z-alkenyl)-2-acyl-sn-glycero-3-phospholipid (plasmalogen).
Justification: The anaerobic bacterial plasmalogen synthases (PlsA/PlsR, single-chain PlsA) form the vinyl-ether bond reductively from an ester. This is chemically distinct from both existing related terms: GO:0047159 "plasmalogen synthase activity" is an acyl-CoA acyltransferase reaction (EC 2.3.1.25), and the aerobic plasmanylethanolamine desaturase acts on an ether, not an ester. These enzymes are widespread in gut anaerobes and lactic acid bacteria, and they currently have no specific MF term. The definition describes only the overall conversion, which heterologous expression demonstrates. The proposed mechanism (an ATP-dependent one-electron reduction to a ketyl radical, a second reduction, then dehydration, by analogy with BCR/HAD enzymes) belongs in a term comment. The electron donor and the stoichiometry are unknown, and no Rhea reaction or EC number exists. Matching GO new-term and GO:0047159 relabelling requests have been drafted.
Parent term: oxidoreductase activity
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0008611 ether lipid biosynthetic process | ISS PMID:41427725 Characterization of plasmalogen production in facultative an... | NEW | Summary: Plasmalogen (vinyl-ether phospholipid) biosynthesis. The 96.6%-identical L. cremoris PlsA is sufficient to produce plasmalogens in E. coli, and 4 of 5 L. cremoris strains tested make plasmalogens natively. Reason: GOA has no annotations for Q9CDI2. Expressing L. cremoris ATCC BAA-493 plsA (LACR_2543) in E. coli gave plasmalogens, and the empty vector gave none (PMID:41427725). The E. faecalis single-chain PlsA (67.3% identical) and the C. perfringens PlsA/PlsR pair behave the same way, and the C. perfringens operon deletion abolishes plasmalogens (PMID:33350306). The protein performs the step that forms the defining vinyl-ether bond, so it participates in the process; it is not merely required for it. This is the same footing on which the aerobic vinyl-ether-forming enzyme CarF of Myxococcus xanthus carries this term. GO has no plasmalogen-specific biosynthesis term (the only child of GO:0008611 is PAF biosynthesis), so the ether lipid term is the most specific available. One caveat: the L. cremoris type strain JCM16167T makes no plasmalogen although it carries a plsA homolog (RU89_GL001778), and no L. lactis subsp. lactis strain was tested (PMID:41427725). Strain-level non-production is most likely regulatory: facultative anaerobes carry a conserved TetR/AcrR-like regulator directly upstream of pls (EF1326 in E. faecalis; PMID:33350306). It does not affect the activity of the enzyme, which the heterologous expression shows directly. Supporting Evidence: PMID:41427725 Both PlsLc and PlsBs produced plasmalogens, as evidenced by the detection of aldehydes in the lipid extracts after acid hydrolysis PMID:41427725 Notably, of the five L. cremoris strains tested, only the type strain JCM16167T did not produce plasmalogen. PMID:33350306 a TetR/AcrR-like transcriptional regulator (EF1326) directly upstream of the pls gene (EF1327) PMID:41427725 These were named plsAK4 (4,248 bp), plsABAA493 (4,311 bp), and plsAsuis (4,920 bp), respectively. PMID:33350306 we observed plasmalogen production in E. coli harboring the pPlsEF plasmid file:LACLA/yxcA/yxcA-bioinformatics/RESULTS.md Q9CDI2 is a full-length, single-chain plasmalogen synthase (PlsA/PlsAR architecture Act1-Act2-Red1-Red2). |
| GO:0051539 4 iron, 4 sulfur cluster binding | ISS PMID:33350306 Plasmalogen Biosynthesis by Anaerobic Bacteria: Identificati... | NEW | Summary: Predicted [4Fe-4S] cluster binding by the Act domains. This is a BCR/HAD family property, and the ligating cysteines are conserved, but no cluster has been observed on any PlsA. Reason: BCR/HAD activators (component A) bind a [4Fe-4S] cluster that mediates the ATP-coupled electron transfer. PlsA Act1 and Act2 conserve the cysteines used for cluster ligation (PMID:33350306). In Q9CDI2, 8 of the 9 cysteines in residues 1-620 are conserved in both E. faecalis and C. perfringens PlsA. In Megasphaera elsdenii MeHAD, a combined mutant of the four predicted cluster-ligand cysteines (Cys125, Cys164, Cys445 and Cys484) makes no plasmalogen (PMID:37348645). These correspond to the conserved C126, C165, C445 and C484 of Q9CDI2. It is proposed as a supporting annotation and is not part of core_functions: no spectroscopic or structural evidence of the cluster exists for any PlsA. Supporting Evidence: PMID:33350306 Act1 and Act2 also share conserved cysteines for iron–sulfur cluster ligation with HAD and BCR activation domains PMID:37348645 The four-cysteine (Cys125, Cys164, Cys445 and Cys484) site-mutant of MeHAD, which were predicted binding to the [4Fe-4S] cluster, was unable to synthesize plasmalogens file:LACLA/yxcA/yxcA-bioinformatics/RESULTS.md All four Q9CDI2 positions are among the eight Act-region cysteines conserved in EF1327 and *C. perfringens* PlsA file:LACLA/yxcA/yxcA-bioinformatics/RESULTS.md both EF1327 and *C. perfringens* PlsA (C126, C165, C445, C449, C484, C606, C609, C613) file:LACLA/yxcA/yxcA-bioinformatics/RESULTS.md Of the nine cysteines in Q9CDI2 residues 1-620, eight align to cysteine in both EF1327 and *C. perfringens* PlsA |
Loading supporting content…
Download this section (compressed HTML)Q: Should GO add an MF term for reductive, ester-to-vinyl-ether plasmalogen synthase activity (PlsA/PlsR)? The existing GO:0047159 "plasmalogen synthase activity" names an unrelated acyltransferase reaction, and electronic pipelines may map PlsA onto it by name.
Suggested experts: GO editors (lipid metabolism)
Q: Is the oxygen tolerance of Lactococcus PlsA (aerobic plasmalogen production in E. coli) a property of the enzyme's iron-sulfur cluster environment, and does L. lactis subsp. lactis make plasmalogens during aerobic growth?
Suggested experts: Iron-sulfur enzyme biochemists, Lactic acid bacteria physiologists
Experiment: Delete yxcA in L. lactis IL1403 and measure plasmalogens (DMA by GC-MS, LC-MS/MS of plasmenyl species) under aerobic and anaerobic growth. This would establish that this ortholog is required in its native host, rather than inferring it from heterologous expression of the L. cremoris gene.
Type: Gene deletion and lipidomics
Experiment: Purify PlsA anaerobically, characterize the iron-sulfur clusters (EPR, Mossbauer), and reconstitute activity on diacyl phosphatidylethanolamine with ATP and reduced ferredoxin or Ti(III) citrate. This would define the electron donor, the ATP stoichiometry and the substrate scope.
Type: In vitro enzyme assay
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)