FAE1 (Thlaspi arvense, field pennycress) — curation notes

Identity

• UniProt V9XY07 (TrEMBL, 506 aa), gene name FAE1; cloned in a Brassicaceae-wide FAE1 survey
  PMID:24358289.
• Chosen over the reference-proteome entry because it carries the gene name and literature. The
  reference proteome (UP000836841) entry is A0AAU9T3A1 / TAV2_LOCUS26079; it differs from V9XY07 at
  1 of 506 positions (identical to a third entry, A0A0S2SVW7). All three are the same gene
  (pairwise comparison of UniProt FASTA, this session).
• InterPro IPR012392 (3-ketoacyl-CoA synthase), IPR013601 (FAE1/type III PKS domain), PANTHER
  PTHR31561. Plant KCS family, ortholog of Arabidopsis FAE1/KCS18 (genes/ARATH/FAE1).

Function

• Condensing enzyme (3-ketoacyl-CoA synthase) of the ER acyl-CoA elongase: condenses malonyl-CoA
  with C18:1/C20:1-CoA, the chain-length-determining first step producing eicosenoic (20:1) and
  erucic (22:1) acids.
• Wild pennycress seed oil is ~35-39% erucic acid, mostly in TAG
  PMID:27889523.
  TaFAE1 is transcriptionally controlled, highly expressed early in seed development
  PMID:27889523.
• Heterologous expression: pennycress FAE1 in Arabidopsis Col-0 gave a 3-4-fold increase in erucic acid;
  substrate preference for eicosenoyl over oleoyl
  PMID:32740897
  (abstract only).
• Loss of function in pennycress itself: CRISPR fae1-3/-4/-5 alleles abolish erucic acid and nearly
  abolish eicosenoic acid in seed TAG
  PMID:30230695.
• fae1 plants grow normally; embryos accumulate more oleic acid and starch; faster germination at 10 °C
  PMID:39657724.
• fae1 is the base of stacked high-oleic genotypes (fad2 fae1 ~90% oleic; rod1 fae1 ~60%)
  PMID:33968108
  and of the domesticated "double-low" pennycress lines PMID:41578087.

Curation decisions (summary)

• MF fatty acid elongase activity (GO:0009922; defined by the KCS condensation reaction): ACCEPT.
• BP fatty acid biosynthetic process: MODIFY to very long-chain fatty acid biosynthetic process (GO:0042761).
  NEW IMP-grounded annotation for GO:0042761 from PMID:30230695.
• CC membrane: MODIFY to ER membrane; ER (ARBA): ACCEPT. No pennycress localization data; inferred
  from the conserved ER elongase complex (Arabidopsis KCS18 review).
• Generic acyltransferase parents: KEEP_AS_NON_CORE (true but uninformative; the specific MF is present).
• Not proposed: triglyceride biosynthetic process. FAE1 makes the acyl-CoA that DGAT1 etc. incorporate;
  FAE1 does none of the acylation steps.
• Not proposed: cuticular wax / suberin. FAE1 is the seed-specific KCS; epidermal VLCFA synthesis uses
  other KCSs (e.g. CER6/KCS6) in Arabidopsis; no pennycress data.