LPXC5 (At1g25210) is one of five tandem, near-identical Arabidopsis genes for UDP-3-O-acyl-N-acetylglucosamine deacetylase (LpxC). LpxC is the zinc-dependent enzyme that removes the N-acetyl group from UDP-3-O-[(3R)-3-hydroxyacyl]-GlcNAc, the committed step of the bacterial-type (Raetz) lipid A pathway. Its 326-aa canonical product is identical in sequence to AtLpxC1.1 (LPXC1). It has a mitochondrial transit peptide and conserves every E. coli LpxC zinc ligand and catalytic residue. No experiment has targeted LPXC5 on its own. RNAi against all five cluster genes lowers the lipid A precursor lipid X, and the identical AtLpxC1.1 protein localises to mitochondria. Which copy contributes the activity in vivo is unknown. Knock-down plants grow normally, and the final plant lipid A-like product and its role are unknown.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: Mitochondrion (is_active_in) from the plant LpxC PAINT node PTN008658623. Reason: AtLpxC1.1-GFP is mitochondrial, and the other Lpx enzymes and the lipid X pool are mitochondrial too. The canonical LPXC5 protein is identical in sequence to AtLpxC1.1 (LPXC1, At1g24793), the variant used for the GFP fusion in Li et al. 2011. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN008658623 · plant mitochondrial LpxC node SUPPORTS TRANSFER Plant-specific node; mitochondrial targeting is shown for AtLpxC1.1-GFP, whose sequence is identical to every canonical AtLpxC product. Supporting Evidence: PMID:21709257 The GFP fluorescence from the full-length GFP fusions of AtLpxA and AtLpxC1.1 localized in mitochondria PMID:21709257 the Lpx and KdtA proteins are expressed and targeted to mitochondria file:ARATH/LPXC1/LPXC1-bioinformatics/RESULTS.md are all 326 aa and are identical to each other |
| GO:0005739 mitochondrion | IDA PMID:21709257 Pathway for lipid A biosynthesis in Arabidopsis thaliana res... | ACCEPT | Summary: Mitochondrion from the C-terminal GFP fusion of full-length AtLpxC1.1 (35S promoter) in Arabidopsis roots, co-localised with MitoTracker (Li et al. 2011). Reason: The experiment used AtLpxC1.1 from LPXC1. The canonical LPXC5 protein is identical in sequence to AtLpxC1.1 (LPXC1, At1g24793), the variant used for the GFP fusion in Li et al. 2011. The GFP result therefore applies directly to the protein this locus encodes, though not to whether this locus is expressed natively. UniProt attributed the result to all five entries for this reason. Supporting Evidence: PMID:21709257 The GFP fluorescence from the full-length GFP fusions of AtLpxA and AtLpxC1.1 localized in mitochondria PMID:21709257 the Lpx and KdtA proteins are expressed and targeted to mitochondria |
| GO:0005739 mitochondrion | IEA GO_REF:0000120 | ACCEPT | Summary: Mitochondrion from the UniProt subcellular-location mapping (SL-0173), whose location line cites Li et al. 2011. Reason: Consistent with the GFP localisation of AtLpxC1.1 and with UniProt's mitochondrial transit peptide (residues 1-21, from mitochondrial N-terminomics, PMID:25732537). The canonical LPXC5 protein is identical in sequence to AtLpxC1.1 (LPXC1, At1g24793), the variant used for the GFP fusion in Li et al. 2011. Supporting Evidence: file:ARATH/LPXC5/LPXC5-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion PMID:21709257 The GFP fluorescence from the full-length GFP fusions of AtLpxA and AtLpxC1.1 localized in mitochondria |
| GO:0009245 lipid A biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: Lipid A biosynthetic process, propagated by PAINT from the LpxC node PTN002134692 (E. coli LpxC). Flagged by Wei et al. 2020 (RAR) as a probable plant misannotation; that flag is refuted. Reason: LpxC catalyses the committed step of the Raetz pathway. Arabidopsis has the whole pathway (LpxA, LpxC, LpxD, LpxB, LpxK, KdtA), and family-wide AtLpxC RNAi lowered lipid X and placed LpxC upstream of LpxB in planta. The plant end product is unknown, so the term describes the conserved precursor pathway. The low taxon rate-ratio reflected sparse curation of a minor, non-essential plant pathway. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN002134692 · LpxC deacetylase ancestral node SUPPORTS TRANSFER The Arabidopsis LpxC copies are full-length family members with every E. coli Zn(2+) ligand and catalytic residue conserved; no evidence of loss of function for the canonical product. UniProtKB:P0A725 · E. coli LpxC SUPPORTS TRANSFER Biochemically and structurally characterised Zn-dependent LpxC; the committed lipid A step in E. coli. Supporting Evidence: PMID:21709257 our work demonstrates that plants synthesize lipid A precursors using the same enzymatic pathway present in E. coli PMID:21709257 The lipid X level decreased in AtLpxC-RNAi transgenic plants to approximately 37% of the amount present in the Col-0 wild type PMID:21709257 accumulation of lipid X in the atlpxb-1 mutant was greatly attenuated by suppressing the transcription of the AtLpxC genes, consistent with the proposal that LpxC functions before LpxB PMID:21709257 The end products of the plant lipid A pathway remain unknown. |
| GO:0009245 lipid A biosynthetic process | IEA GO_REF:0000002 | ACCEPT | Summary: Lipid A biosynthetic process from InterPro2GO (IPR004463/IPR011334/IPR015870 LpxC family and domains). Reason: Same claim as the IBA row; supported in planta by AtLpxC RNAi lipidomics. The RAR misannotation flag (PMID:32470107) does not hold for this pathway. Supporting Evidence: file:ARATH/LPXC5/LPXC5-uniprot.txt IPR004463; UDP-acyl_GlcNac_deAcase PMID:21709257 our work demonstrates that plants synthesize lipid A precursors using the same enzymatic pathway present in E. coli PMID:21709257 The lipid X level decreased in AtLpxC-RNAi transgenic plants to approximately 37% of the amount present in the Col-0 wild type |
| GO:0009507 chloroplast | ISM GO_REF:0000122 | REMOVE | Summary: Chloroplast predicted by AtSubP sequence-based targeting analysis (TAIR). Reason: Contradicted by experiment. In leaf mesophyll the AtLpxC1.1-GFP signal (identical protein) formed dots that did not co-localise with chloroplasts, root signal co-localised with MitoTracker, and every Lpx enzyme tested was mitochondrial. Lipid X is found in chloroplast fractions of atlpxb-1, but at much lower levels than in mitochondria, and that is the lipid, not the enzyme. Location is mitochondrion. Supporting Evidence: PMID:21709257 In mesophyll cells, GFP signals were shown as 1 μm dots, but were not colocalized with chloroplasts (data not shown). PMID:21709257 The GFP fluorescence from the full-length GFP fusions of AtLpxA and AtLpxC1.1 localized in mitochondria PMID:21709257 Lipid X levels in mitochondria were 3- and 48-fold higher than in chloroplasts or whole cell homogenates, respectively. |
| GO:0103117 UDP-3-O-acyl-N-acetylglucosamine deacetylase activity | IBA GO_REF:0000033 | ACCEPT | Summary: UDP-3-O-acyl-GlcNAc deacetylase activity propagated by PAINT from the LpxC node PTN002134692 (E. coli LpxC and other bacterial members). Reason: Core function. The canonical protein is a full-length LpxC family member (36% identity to E. coli LpxC) that conserves the Zn(2+) ligands, D246 and the proton donor H265 (E. coli numbering). Family-wide RNAi lowered lipid X in planta, as expected for loss of the LpxC step. No in vitro assay of an Arabidopsis LpxC exists, so the activity is inferred, but nothing argues against the node placement. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN002134692 · LpxC deacetylase ancestral node SUPPORTS TRANSFER The Arabidopsis LpxC copies are full-length family members with every E. coli Zn(2+) ligand and catalytic residue conserved; no evidence of loss of function for the canonical product. UniProtKB:P0A725 · E. coli LpxC SUPPORTS TRANSFER Biochemically and structurally characterised Zn-dependent LpxC; the committed lipid A step in E. coli. Supporting Evidence: file:ARATH/LPXC1/LPXC1-bioinformatics/RESULTS.md conserved: H79 -> H109, H238 -> H281, D242 -> D285, D246 -> D289, H265 -> H313. PMID:21709257 Previous studies of E. coli LpxC had shown that three amino acid residues (H238, D246, and H265) in the C-terminal region of the protein are critical for activity PMID:21709257 The lipid X level decreased in AtLpxC-RNAi transgenic plants to approximately 37% of the amount present in the Col-0 wild type |
| GO:0103117 UDP-3-O-acyl-N-acetylglucosamine deacetylase activity | IEA GO_REF:0000120 | ACCEPT | Summary: UDP-3-O-acyl-GlcNAc deacetylase activity from combined InterPro (IPR004463 LpxC family) / EC 3.5.1.108 / RHEA:67816 mapping. Reason: Same claim as the IBA row. The InterPro family signature covers the whole catalytic fold and all E. coli catalytic residues are conserved. Supporting Evidence: file:ARATH/LPXC5/LPXC5-uniprot.txt IPR004463; UDP-acyl_GlcNac_deAcase file:ARATH/LPXC5/LPXC5-uniprot.txt Belongs to the LpxC family. file:ARATH/LPXC1/LPXC1-bioinformatics/RESULTS.md conserved: H79 -> H109, H238 -> H281, D242 -> D285, D246 -> D289, H265 -> H313. |
| GO:0103117 UDP-3-O-acyl-N-acetylglucosamine deacetylase activity | IMP PMID:21709257 Pathway for lipid A biosynthesis in Arabidopsis thaliana res... | ACCEPT | Summary: UDP-3-O-acyl-GlcNAc deacetylase activity from the AtLpxC-RNAi lines of Li et al. 2011, which lowered lipid X to ~37% of wild type and suppressed lipid X accumulation in atlpxb-1. Reason: The RNAi construct and RT-PCR primers targeted sequence shared by all five tandem AtLpxC genes, so the phenotype belongs to the gene family collectively and cannot be assigned to this locus alone; the authors state that it is unclear which copy is active. The canonical LPXC5 protein is identical in sequence to AtLpxC1.1 (LPXC1, At1g24793), the variant used for the GFP fusion in Li et al. 2011. Because the five canonical products are identical, the inference that the protein has the activity applies equally to each locus. The phenotype is indirect (a downstream metabolite, not an enzyme assay) but is exactly what loss of LpxC predicts, and it agrees with the orthology-based rows. Supporting Evidence: PMID:21709257 To suppress transcription of the five closely linked AtLpxC genes PMID:21709257 The lipid X level decreased in AtLpxC-RNAi transgenic plants to approximately 37% of the amount present in the Col-0 wild type PMID:21709257 accumulation of lipid X in the atlpxb-1 mutant was greatly attenuated by suppressing the transcription of the AtLpxC genes, consistent with the proposal that LpxC functions before LpxB PMID:21709257 However, it remains unclear which of the closely related AtLpxC enzymes is functional in vivo file:ARATH/LPXC1/LPXC1-bioinformatics/RESULTS.md are all 326 aa and are identical to each other |
| GO:0103117 UDP-3-O-acyl-N-acetylglucosamine deacetylase activity | ISS GO_REF:0000024 | ACCEPT | Summary: UDP-3-O-acyl-GlcNAc deacetylase activity by UniProt sequence-similarity transfer from E. coli LpxC (P0A725). Reason: Same claim as the IBA/IEA rows; the active site is fully conserved relative to the source enzyme. Supporting Evidence: file:ARATH/LPXC5/LPXC5-uniprot.txt Belongs to the LpxC family. file:ARATH/LPXC1/LPXC1-bioinformatics/RESULTS.md conserved: H79 -> H109, H238 -> H281, D242 -> D285, D246 -> D289, H265 -> H313. |
| GO:2001289 obsolete lipid X metabolic process | IEA GO_REF:0000117 | MODIFY | Summary: Lipid X metabolic process from ARBA rule ARBA00027142. The term is obsolete (QuickGO: obsolete, no replacement given). Reason: The biology is right: LpxC acts upstream of lipid X (2,3-diacylglucosamine 1-phosphate) in the lipid A pathway. Because the term is obsolete, it becomes lipid A biosynthetic process, which the gene already carries by IBA/IEA. No lipid IVA-specific process term exists. Proposed replacements: lipid A biosynthetic process Supporting Evidence: PMID:21709257 The lipid X level decreased in AtLpxC-RNAi transgenic plants to approximately 37% of the amount present in the Col-0 wild type PMID:21709257 our work demonstrates that plants synthesize lipid A precursors using the same enzymatic pathway present in E. coli |
| GO:2001289 obsolete lipid X metabolic process | IMP PMID:21709257 Pathway for lipid A biosynthesis in Arabidopsis thaliana res... | MODIFY | Summary: Lipid X metabolic process (obsolete term) from the AtLpxC-RNAi lipidomics of Li et al. 2011. Reason: The experiment is sound: lipid X fell to ~37% of wild type, and RNAi suppressed lipid X accumulation in atlpxb-1. The replacement for the obsolete term is lipid A biosynthetic process, the pathway in which lipid X is an intermediate. RNAi targeted all five AtLpxC genes, so the evidence is family-level. The canonical LPXC5 protein is identical in sequence to AtLpxC1.1 (LPXC1, At1g24793), the variant used for the GFP fusion in Li et al. 2011. Proposed replacements: lipid A biosynthetic process Supporting Evidence: PMID:21709257 The lipid X level decreased in AtLpxC-RNAi transgenic plants to approximately 37% of the amount present in the Col-0 wild type PMID:21709257 accumulation of lipid X in the atlpxb-1 mutant was greatly attenuated by suppressing the transcription of the AtLpxC genes, consistent with the proposal that LpxC functions before LpxB PMID:21709257 To suppress transcription of the five closely linked AtLpxC genes |
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Download this section (compressed HTML)Q: Which of the five identical AtLpxC loci are transcribed and translated in planta, and in which tissues? With identical coding sequences, does the activity come from one copy or several?
Q: Do the AtLpxC copies differ in UTRs or promoters in ways that separate their expression, or are they kept identical by gene conversion?
Q: Does recombinant mature AtLpxC deacetylate UDP-3-O-[(3R)-3-hydroxymyristoyl]-GlcNAc, and is it sensitive to LpxC inhibitors such as CHIR-090?
Experiment: Express the mature protein (without residues 1-21) and assay deacetylation of UDP-3-O-(R-3-hydroxymyristoyl)-GlcNAc by LC-MS. Test complementation of a conditional E. coli lpxC strain; use the AtLpxC1.2-type truncation (lacking H281/D285/D289/H313) as a negative control.
Hypothesis: The 326-aa AtLpxC product is an active Zn-dependent UDP-3-O-acyl-GlcNAc deacetylase.
Type: in vitro enzyme assay and complementation
Experiment: Use long-read RNA-seq with UTR-anchored, locus-specific primers to assign transcripts to loci. Delete individual loci and the whole 68-kb cluster with CRISPR/Cas9, then measure lipid X and lipid IVA by LC-ESI/MS.
Hypothesis: Only a subset of the five tandem AtLpxC loci contributes lipid X synthesis in vivo.
Type: locus-resolved expression and genome editing
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