LPXD2 (At4g21220) encodes the predominant Arabidopsis UDP-3-O-acylglucosamine N-acyltransferase (LpxD), the third enzyme of a plant lipid A precursor pathway that mirrors the Escherichia coli Raetz pathway (LpxA, LpxC, LpxD, LpxB, LpxK, KdtA). By orthology to bacterial LpxD it transfers an (R)-3-hydroxyacyl chain from acyl carrier protein to the 2-amino group of UDP-3-O-acyl-glucosamine, forming UDP-2,3-diacylglucosamine, the precursor of lipid X (2,3-diacylglucosamine 1-phosphate). It is a nuclear-encoded hexapeptide-repeat (left-handed beta-helix) acyltransferase with an N-terminal mitochondrial transit peptide, and an N-terminal GFP fusion is targeted to mitochondria. Lipid X is undetectable in atlpxd2 null seedlings, whereas loss of the paralog LPXD1 has no effect, so LPXD2 supplies nearly all LpxD activity in seedlings. Null plants grow normally under laboratory conditions. The plant lipid A-like end product and its role, possibly in mitochondrial or chloroplast outer membranes or in signalling, are unknown.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005737 cytoplasm | IEA GO_REF:0000117 | MODIFY | Summary: Cytoplasm, from an ARBA machine-learning rule. Reason: True in the GO sense (mitochondria are part of the cytoplasm) but less specific than the evidence supports. A 5'-terminal LPXD2-GFP fusion shows a mitochondrial pattern and the protein has a predicted N-terminal mitochondrial transit peptide, so the informative term is mitochondrion (GO:0005739), which the gene already carries from IDA, IBA and IEA rows. Proposed replacements: mitochondrion Supporting Evidence: PMID:21709257 However, 5β²-terminal fusions of AtLpxD1, AtLpxD2, AtLpxB, and AtLpxK to GFP showed the same mitochondrial pattern as full-length AtLpxA and AtLpxC |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: Mitochondrion propagated by PAINT from the plant LpxD node PTN008106513, whose experimental grounding is the GFP localisation of both Arabidopsis LpxD paralogs. Reason: The node is a plant-specific mitochondrial LpxD clade. The target appearing among its own sources reflects its IDA localisation, which is expected and not circular. Consistent with the GFP data, the predicted transit peptide and the mitochondrial enrichment of the pathway intermediate lipid X. Supporting Evidence: PMID:21709257 However, 5β²-terminal fusions of AtLpxD1, AtLpxD2, AtLpxB, and AtLpxK to GFP showed the same mitochondrial pattern as full-length AtLpxA and AtLpxC file:ARATH/LPXD2/LPXD2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:21709257} |
| GO:0005739 mitochondrion | IDA PMID:21709257 Pathway for lipid A biosynthesis in Arabidopsis thaliana res... | ACCEPT | Summary: Mitochondrion from a 5'-terminal LPXD2-GFP fusion imaged with MitoTracker in root cells of transgenic Arabidopsis (Li et al. 2011). Reason: Direct experimental localisation. The full-length fusion was too dim to image, so the result rests on the N-terminal region fused to GFP, which shows that the presequence is a functional mitochondrial targeting signal. Lipid X, the product of the LpxD-dependent steps, is enriched in mitochondria relative to chloroplasts and whole homogenates. Mitochondrion is the right level of precision; no sub-mitochondrial location has been tested. Supporting Evidence: PMID:21709257 However, 5β²-terminal fusions of AtLpxD1, AtLpxD2, AtLpxB, and AtLpxK to GFP showed the same mitochondrial pattern as full-length AtLpxA and AtLpxC PMID:21709257 Full-length GFP fusions of AtLpxD1, AtLpxD2, AtLpxB, and AtLpxK did not emit sufficient GFP fluorescence to permit localization. PMID:21709257 Lipid X levels in mitochondria were 3- and 48-fold higher than in chloroplasts or whole cell homogenates, respectively. |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | ACCEPT | Summary: Mitochondrion from the UniProt subcellular location mapping; the UniProt line is backed by Li et al. 2011 (ECO:0000269). Reason: Same claim as the IDA row; supported by GFP localisation. Supporting Evidence: file:ARATH/LPXD2/LPXD2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:21709257} PMID:21709257 However, 5β²-terminal fusions of AtLpxD1, AtLpxD2, AtLpxB, and AtLpxK to GFP showed the same mitochondrial pattern as full-length AtLpxA and AtLpxC |
| GO:0009245 lipid A biosynthetic process | IEA GO_REF:0000002 | ACCEPT | Summary: Lipid A biosynthetic process from the InterPro2GO mapping of IPR007691 (LpxD family). Flagged by Wei et al. 2020 (RAR) as a probable plant misannotation; that flag is refuted for this gene. Reason: Core process, and the only GOA row for it rests on InterPro2GO, but gene-specific experimental evidence supports it directly. LPXD2 catalyses a step of the pathway itself (participation, not mere requirement): in atlpxd2-1 null seedlings lipid X, the intermediate two steps downstream, is undetectable, and atlpxd2-1 strongly lowers the lipid X that accumulates in atlpxb-1. This places LPXD2 between LpxC and LpxB, as for E. coli LpxD. The comparator check is satisfied because the term's members are the pathway enzymes themselves (E. coli LpxA, LpxC, LpxD, LpxB, LpxK, KdtA), and the Arabidopsis LpxA and KdtA reviews accept it on the same kind of evidence. The plant end product is unknown, but the precursor steps are shared with E. coli, so the RAR flag reflected sparse plant curation rather than absence of the pathway. Supporting Evidence: PMID:21709257 lipid X was undetectable in the atlpxd2-1 mutant compared with its parental plant PMID:21709257 indicating that AtLpxD2 is the predominant UDP-3- O -acyl-GlcN N -acyltransferase PMID:21709257 Introducing the atlpxd2-1 mutation into the atlpxb-1 mutant background significantly lowered lipid X levels PMID:21709257 our work demonstrates that plants synthesize lipid A precursors using the same enzymatic pathway present in E. coli PMID:21709257 the genes encoding AtLpxA, AtLpxC, and AtLpxD2 are required for the efficient production of lipid X |
| GO:0009507 chloroplast | ISM GO_REF:0000122 | REMOVE | Summary: Chloroplast predicted by AtSubP sequence analysis (TAIR). Reason: Contradicted by experiment. In mesophyll cells the Lpx-GFP fusions formed punctate signals that did not colocalise with chloroplasts, and in roots the LPXD2 fusion showed the mitochondrial pattern. The N-terminal presequence is a predicted mitochondrial transit peptide. Some lipid X is found in chloroplasts, which the authors interpret as transport of the lipid, not as a chloroplast location for the enzymes. Supporting Evidence: PMID:21709257 In mesophyll cells, GFP signals were shown as 1 ΞΌm dots, but were not colocalized with chloroplasts PMID:21709257 However, 5β²-terminal fusions of AtLpxD1, AtLpxD2, AtLpxB, and AtLpxK to GFP showed the same mitochondrial pattern as full-length AtLpxA and AtLpxC PMID:21709257 These findings suggest that lipid A precursors are synthesized in mitochondria and may be transported from mitochondria to chloroplasts. |
| GO:0016747 acyltransferase activity, transferring groups other than amino-acyl groups | IEA GO_REF:0000002 | MODIFY | Summary: Acyltransferase activity (non-aminoacyl) from InterPro2GO mapping of IPR007691 (LpxD). Reason: Correct but general. IPR007691 is the LpxD family itself, and LPXD2 is the predominant Arabidopsis LpxD by mutant chemistry, so the informative term is UDP-3-O-[(3R)-3-hydroxyacyl]-glucosamine N-acyltransferase activity (GO:0103118), which the gene already carries from IBA, IEA and IMP rows. Proposed replacements: UDP-3-O-[(3R)-3-hydroxyacyl]-glucosamine N-acyltransferase activity Supporting Evidence: file:ARATH/LPXD2/LPXD2-uniprot.txt Belongs to the transferase hexapeptide repeat family. LpxD subfamily. PMID:21709257 indicating that AtLpxD2 is the predominant UDP-3- O -acyl-GlcN N -acyltransferase |
| GO:0103118 UDP-3-O-[(3R)-3-hydroxyacyl]-glucosamine N-acyltransferase activity | IBA GO_REF:0000033 | ACCEPT | Summary: LpxD activity propagated by PAINT from node PTN000501148, seeded by E. coli LpxD (P21645) and the Arabidopsis LpxD paralogs. Reason: Core molecular function. LPXD2 is inside the LpxD clade, keeps the catalytic histidine and the acyl-ACP-binding arginine (E. coli His239 and Arg293), and its own mutant phenotype (loss of lipid X) is part of the descendant evidence for the node, so the IBA additionally says the function is inherited. No in vitro assay of LPXD2 has been reported, so the activity rests on orthology plus in planta genetics (hence "Probable" in UniProt). Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000501148 Β· LpxD ancestral node SUPPORTS TRANSFER LPXD2 is a full-length LpxD with conserved catalytic and acyl-ACP-binding residues; its mutant loses lipid X, matching the inherited activity. UniProtKB:P21645 Β· E. coli LpxD SUPPORTS TRANSFER Biochemically and structurally characterised LpxD. Supporting Evidence: PMID:21709257 these proteins share 41 and 34% identity with E. coli LpxD ( Table 1 ), with conservation of key catalytic residues PMID:21709257 R293 is conserved between E. coli LpxD and AtLpxD2, but is replaced by lysine in AtLpxD1. file:ARATH/LPXD1/LPXD1-bioinformatics/RESULTS.md EcLpxD catalytic H239 -> AtLpxD1 H217, AtLpxD2 H216 (both conserved; these match the UniProt ACT_SITE positions 217 and 216). PMID:21709257 lipid X was undetectable in the atlpxd2-1 mutant compared with its parental plant |
| GO:0103118 UDP-3-O-[(3R)-3-hydroxyacyl]-glucosamine N-acyltransferase activity | IEA GO_REF:0000116 | ACCEPT | Summary: LpxD activity from the Rhea mapping of the UniProt catalytic activity line (RHEA:53836). Reason: Same claim as the IBA and IMP rows; supported by orthology and by loss of lipid X in atlpxd2 mutants. Supporting Evidence: PMID:21709257 indicating that AtLpxD2 is the predominant UDP-3- O -acyl-GlcN N -acyltransferase PMID:21709257 these proteins share 41 and 34% identity with E. coli LpxD ( Table 1 ), with conservation of key catalytic residues |
| GO:0103118 UDP-3-O-[(3R)-3-hydroxyacyl]-glucosamine N-acyltransferase activity | IMP PMID:21709257 Pathway for lipid A biosynthesis in Arabidopsis thaliana res... | ACCEPT | Summary: LpxD activity by mutant phenotype (Li et al. 2011); lipid X is undetectable in atlpxd2-1 seedlings. Reason: The mutant chemistry is specific to the LpxD step. Lipid X, the intermediate downstream of LpxD, disappears in atlpxd2-1 and is strongly reduced when atlpxd2-1 is combined with atlpxb-1, while loss of the paralog LPXD1 has no effect. The authors conclude that LPXD2 is the primary UDP-3-O-acyl-GlcN N-acyltransferase. Activity is inferred from loss-of-function chemistry plus orthology rather than from an enzyme assay, which is what an IMP asserts. Supporting Evidence: PMID:21709257 lipid X was undetectable in the atlpxd2-1 mutant compared with its parental plant PMID:21709257 Introducing the atlpxd2-1 mutation into the atlpxb-1 mutant background significantly lowered lipid X levels PMID:21709257 These results suggest that AtLpxD2 is the primary UDP-3- O -acyl-GlcN N -acyltransferase in Arabidopsis |
| GO:2001289 obsolete lipid X metabolic process | IBA GO_REF:0000033 | MODIFY | Summary: Obsolete term "lipid X metabolic process" propagated from the plant LpxD node PTN008106513. Reason: QuickGO marks GO:2001289 obsolete ("made in error and is an unnecessary grouping term") with no replacement. The biology behind the row is sound for LPXD2, which catalyses a step toward lipid X, and the appropriate current term is lipid A biosynthetic process (GO:0009245), accepted in this review. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN008106513 Β· plant LpxD node SOURCE STALE OR MISSING The biology transfers to LPXD2, but the propagated term is now obsolete; lipid A biosynthetic process is the current term. Proposed replacements: lipid A biosynthetic process Supporting Evidence: PMID:21709257 lipid X was undetectable in the atlpxd2-1 mutant compared with its parental plant PMID:21709257 the genes encoding AtLpxA, AtLpxC, and AtLpxD2 are required for the efficient production of lipid X |
| GO:2001289 obsolete lipid X metabolic process | IMP PMID:21709257 Pathway for lipid A biosynthesis in Arabidopsis thaliana res... | MODIFY | Summary: Obsolete term "lipid X metabolic process" from loss of lipid X in the atlpxd2-1 null mutant (Li et al. 2011). Reason: The experiment is sound and specific (lipid X undetectable in atlpxd2-1, and lowered when atlpxd2-1 is combined with atlpxb-1), but GO:2001289 is obsolete without replacement. The finding supports lipid A biosynthetic process (GO:0009245), the pathway in which LPXD2 catalyses the third step. Proposed replacements: lipid A biosynthetic process Supporting Evidence: PMID:21709257 lipid X was undetectable in the atlpxd2-1 mutant compared with its parental plant PMID:21709257 Introducing the atlpxd2-1 mutation into the atlpxb-1 mutant background significantly lowered lipid X levels PMID:21709257 the genes encoding AtLpxA, AtLpxC, and AtLpxD2 are required for the efficient production of lipid X |
Loading supporting contentβ¦
Download this section (compressed HTML)Q: What is the acyl-ACP donor and chain-length preference of LPXD2 in mitochondria, given that the mitochondrial fatty acid synthase is the likely source of (R)-3-hydroxyacyl-ACP?
Q: Why does loss of LPXD2, which removes detectable lipid X, cause no visible phenotype; is the pathway needed only under stress, during pathogen challenge or in specific tissues?
Q: Does LPXD2 form a homotrimer, like bacterial LpxD, and does it hetero-oligomerise with the closely related LPXD1?
Experiment: Express mature LPXD2 (without transit peptide), assay with UDP-3-O-acyl-GlcN and R-3-hydroxymyristoyl-ACP, and test complementation of an E. coli lpxD conditional mutant.
Hypothesis: LPXD2 is a functional LpxD that N-acylates UDP-3-O-(R-3-hydroxymyristoyl)-GlcN using R-3-hydroxyacyl-ACP.
Type: in vitro enzyme assay and bacterial complementation
Experiment: Transform atlpxd2-1 with a genomic LPXD2 construct and quantify lipid X by LC-MRM; isolate a second, Col-0 background atlpxd2 allele.
Hypothesis: Loss of lipid X in atlpxd2-1 is caused by the LPXD2 insertion and not by background effects.
Type: complementation in planta
Experiment: Challenge atlpxd2 mutants with bacterial pathogens and mitochondrial stressors and measure growth, respiration and immune outputs.
Hypothesis: The LPXD2-dependent lipid A-like product has a conditional role in mitochondrial membrane function or defence.
Type: stress and pathogen phenotyping
Loading supporting contentβ¦
Download this section (compressed HTML)Loading supporting contentβ¦
Download this section (compressed HTML)