plsY (yneS, BSU18070; UniProt Q45064) — review notes

Part of projects/LIPID_DIVIDE.md (Part B, acyltransferases that accept both enantiomers).

Sources and search record (2026-11-02)

• No deep-research provider key was available, so no plsY-deep-research-<provider>.md was generated.
• just mod-description-deep-research BACSU plsY was run: skipped, "no MOD provider configured for organism 'BACSU'".
• PubMed searches: "Palyzová glycerol phosphate enantiomers phospholipids bacteria" (4 hits; PMID:35767906 is the
  2022 J Chromatogr A paper cited by Rieche et al. as Palyzova et al. 2022); "Bacillus subtilis essential genes
  Kobayashi 2003" (PMID:12682299).
• Newly cached: PMID:35767906 (abstract only), PMID:12682299 (abstract only; gene lists are in the full text, not cached).
• Read: PMID:42286214 (Rieche 2026, full text), PMID:17645809 (Yoshimura 2007, full text), PMID:17557823
  (Paoletti 2007, abstract), PMID:19282621 (Hara 2008, abstract), the UniProt record, and the PTHR10434 PAINT
  file (for the plsC comparison).
• Not cached / not read: García-Domínguez & Devos 2026 (PMID:42965973); Palyzová et al. 2025 (PG stereoisomers in
  B. tequilensis, cited by Rieche); Lu et al. 2006/2007 (S. pneumoniae PlsY biochemistry).

Function: acyl-phosphate:G3P acyltransferase (first acylation)

• PlsY is the GPAT of the PlsX/PlsY pathway: PlsX converts acyl-ACP to acyl-phosphate, and PlsY transfers the acyl
  group to the sn-1 position of G3P to give LPA PMID:17557823.
• Acyl donor specificity in B. subtilis membranes: PMID:17557823.
• Genetic loss of activity: PMID:19282621 and PMID:19282621
• In vivo block: PMID:17645809; PMID:17557823.
• Essentiality: the IPTG-dependent yneS strain YNESp fails to grow when depleted, and B. subtilis has no plsB
  PMID:17645809; PMID:17645809.
  E. coli plsB rescues plsY repression PMID:19282621.
• G3P is a physiologically limiting substrate in vivo: the yneS-ts phenotype is suppressed by raising intracellular
  G3P (glpD loss, or G3P/glycerol in the medium) PMID:17645809. This is the only in vivo substrate evidence for
  either enantiomer, and it concerns G3P.
• Regulation: inhibited by acyl-CoA (UniProt, ECO:0000269 PMID:17557823). Two-hybrid suggests PlsX–PlsY
  association PMID:19282621 — not used for a
  GO term (protein-binding policy).

Location

• Polytopic integral membrane protein: five predicted TM helices (UniProt FT TRANSMEM, ECO:0000255); "a membrane
  protein around 200 amino acids long" PMID:17645809. Activity resides in the membrane fraction PMID:19282621.
  B. subtilis is a monoderm, so membrane = plasma membrane. Rieche: "Although PlsY is located in the membrane"
  PMID:42286214.

Stereochemistry (the lipid-divide question)

• In vitro, detergent: BsPlsY and EcPlsY acylate G1P and G3P at similar levels [PMID:42286214 "Remarkably, the
  addition of glycerol 3-phosphate, as well as glycerol 1-phosphate, resulted in the substantial production of
  LPA, with only minor differences in quantities over time."; "it appears there is no major preference of either
  PlsY enzyme for G3P/G1P as substrate"].
• In vitro, liposome-reconstituted (closer to native): G3P clearly preferred, and more so for the Bacillus enzyme
  [PMID:42286214 "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"; for EcPlsY
  "Again, the levels of produced (R)-LPA were significantly higher than (S)-LPA, but to a much lesser extent as for
  the Bacillus enzyme."]. No kinetic constants were measured PMID:42286214.
• In vivo observation (Řezanka lab only): G1P and G3P detected in B. subtilis and other Gram-positives, and "the
  presence of both enantiomers in the glycerol backbone of some molecular species of PG was revealed"
  PMID:35767906. The 4:1 G3P:G1P ratio in that abstract refers to the glycerol phosphates detected, not explicitly
  to the PG backbone; Rieche summarise it as 4:1 to 3:1 for membrane backbones. Abstract only; method details (and
  whether headgroup glycerol was excluded — PG's headgroup glycerol is itself sn-1-linked) could not be checked
  beyond "enzymatic cleavage by phospholipase C". Not independently replicated by another group.
• Inference by Rieche: PMID:42286214. "In line with" is not a demonstration.
• G1P source: B. subtilis AraM/EgsA is the only known G1PDH; it supplies G1P for heptaprenylglyceryl phosphate (PcrB).
  Rieche note G1P biosynthesis routes are incompletely known PMID:42286214. No araM knockout or overexpression has been tested for PG backbone chirality.

Judgement (in vivo vs promiscuity)

Applying the ENZYME_SPECIFICITY tiers: G1P acylation by BsPlsY is not noise-level (near G3P levels in detergent),
so it is not the REMOVE tier. But its physiological use is unshown: (1) the membrane-reconstituted assay shows a
significant G3P preference for the Bacillus enzyme, (2) the only in vivo substrate evidence (yneS-ts suppression)
is for G3P, (3) the in vivo heterochirality rests on one lab's abstract-level report, and (4) the G1P pool feeding
PlsY is unidentified. The logical chain "G1P-backbone PG exists + PlsY is the sole GPAT → PlsY acylates G1P in
vivo" is sound if premise 1 holds, and it is the most parsimonious explanation, but premise 1 is unreplicated.

Decision: propose a GO term (acyl-phosphate glycerol-1-phosphate acyltransferase activity) because GO cannot
currently record even the direct in vitro result (an IDA-quality observation for two orthologs), but do NOT put it
in core_functions and do NOT add a NEW annotation. Record the in vivo question as a BIOLOGY knowledge gap. If an
araM/G1P-dependence experiment confirms G1P-backbone lipids pass through PlsY, the term would become a genuine
secondary (KEEP_AS_NON_CORE-level) function.

GOA rows (5)

• GO:0043772 IEA (UniRule): ACCEPT, matches the experimentally established reaction.
• GO:0005886 IBA and IEA: ACCEPT (5 TM helices; activity in membrane fraction; monoderm).
• GO:0008654 IEA, GO:0006644 IEA: MODIFY to GO:0006654 phosphatidic acid biosynthetic process (PlsY catalyses the
  first acylation on the way to PA; precise process supported by knockouts).