LPXB (At2g04560, F4IF99) notes

Deep research could not be run in this environment (provider auth failure); the notes below
come from the cached full text of Li et al. 2011 (PMID:21709257, PMC3136250), the UniProt
record, and PubMed searches.

Identity

• Single-copy Arabidopsis ortholog of E. coli LpxB (lipid-A-disaccharide synthase, EC 2.4.1.182,
  GT19 family, Pfam PF02684 LpxB, PANTHER PTHR30372:SF4) PMID:21709257.
• UniProt: predicted mitochondrial transit peptide 1..58 (ECO:0000255); "Belongs to the LpxB family".

Genetics and lipid chemistry (Li et al. 2011, full text)

• Alleles: atlpxb-1 (SALK_087537), atlpxb-2 (SALK_087529), Col-0 background; homozygous nulls viable,
  no visible phenotype PMID:21709257.
• Lipid X (2,3-diacylglucosamine 1-phosphate; LpxB acceptor substrate) accumulates strongly
  PMID:21709257.
• UDP-2,3-diacyl-GlcN (LpxB donor substrate) is detectable only in atlpxb-1 PMID:21709257.
• The LpxB product (disaccharide 1-phosphate) is seen only downstream, in lpxk and kdta mutants
  PMID:21709257.
• Second allele confirms PMID:21709257.
• Epistasis: LpxC-RNAi and lpxd2 in the lpxb-1 background lower lipid X accumulation, placing LpxB
  after LpxC/LpxD2, as in E. coli.
• No in vitro activity assay and no E. coli complementation was reported for AtLpxB.

Localization

• Full-length AtLpxB-GFP was too dim; a 5'-terminal (N-terminal region) fusion co-localised with
  MitoTracker in roots PMID:21709257.
• In leaf mesophyll the fusion dots did not co-localise with chloroplasts PMID:21709257. So the chloroplast ISM (AtSubP) prediction is not supported for the enzyme.
• Lipid X in atlpxb-1 fractions: mitochondria-enriched PMID:21709257. This is
  the basis of the IMP mitochondrion annotation (substrate pool location, indirect for the enzyme).

RAR context

• Wei et al. 2020 (PMID:32470107) flagged plant lipid A biosynthetic process annotations, including
  LPXB, as misannotations. Refuted by the mutant chemistry above (see projects/RAR_MISANNOTATION.md).

Other literature checked

• PubMed searches ("LpxB/LpxK/lipid A AND Arabidopsis") return no further LpxB-specific work.
  PMID:21896887 (Duncan 2011, mitochondrial outer membrane proteome) discusses lipid A only via KDSB/CKS;
  PMID:28202596 (mtFAS mtHD) reports reduced 3-hydroxytetradecanoic acid (lipid A hallmark) in mtFAS
  mutants, supporting a mitochondrial acyl-ACP source but not about LpxB itself.

Curation decisions

• GO:2001289 lipid X metabolic process is obsolete (QuickGO: "made in error and is an unnecessary
  grouping term", no replacement). The IMP evidence is the experimental basis for lipid A biosynthetic
  process; MODIFY to GO:0009245.
• No NEW rows needed: lipid A biosynthetic process, LpxB activity and mitochondrion are already in GOA;
  the experimental evidence is put in those rows.