KDTA (At5g03770) is a nuclear-encoded, mitochondrially targeted 3-deoxy-D-manno-octulosonic acid (Kdo) transferase of the glycosyltransferase GT30 family, orthologous to the bacterial bifunctional enzyme WaaA/KdtA that transfers two Kdo residues from CMP-Kdo onto the lipid A precursor lipid IVA. It is the single Arabidopsis KdtA and acts in a plant lipid A precursor pathway that mirrors the E. coli Raetz pathway (LpxA, LpxC, LpxD, LpxB, LpxK, KdtA). kdta null mutants accumulate lipid IVA and the upstream disaccharide 1-phosphate but have no visible phenotype. KDTA is not required for incorporation of Kdo into the cell-wall pectin rhamnogalacturonan II. The final plant lipid A-like product and its physiological role, possibly a mitochondrial membrane component or a signalling lipid, remain unknown.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | ACCEPT | Summary: Mitochondrion, from the UniProt subcellular-location mapping; the UniProt location line is backed by the Seveno et al. 2010 GFP-fusion experiment. Reason: AtKDTA-GFP was targeted to mitochondria (Seveno et al. 2010, abstract), and Li et al. 2011 cite this localisation and show that the companion Lpx enzymes and the lipid X pool are mitochondrial. The precise sub-mitochondrial compartment is unknown, so mitochondrion is the appropriate level of precision. Supporting Evidence: PMID:20124190 the fusion protein was demonstrated to be targeted to the mitochondria PMID:21709257 The AtKdtA protein was recently localized to mitochondria of Arabidopsis |
| GO:0005739 mitochondrion | ISM GO_REF:0000122 | ACCEPT | Summary: Mitochondrion predicted by AtSubP sequence-based targeting prediction (TAIR). Reason: The prediction agrees with experimental GFP localisation (Seveno et al. 2010) and the UniProt transit-peptide-bearing precursor annotation. Same claim as the IEA row; accepted consistently. Supporting Evidence: PMID:20124190 the fusion protein was demonstrated to be targeted to the mitochondria |
| GO:0009245 lipid A biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: Lipid A biosynthetic process, propagated by PAINT from node PTN000602593 seeded by E. coli WaaA/KdtA (P0AC75). Flagged by Wei et al. 2020 (RAR) as a probable plant misannotation; that flag is refuted for this gene. Reason: The node placement is sound: AtKdtA is a full-length single-copy GT30 ortholog of E. coli KdtA (34% identity), and gene-specific mutant chemistry supports the inherited function. In atkdta-1 null plants the KdtA acceptor lipid IVA accumulates (detected in no other line) together with the upstream disaccharide 1-phosphate, as predicted for loss of the step after LpxK. Seveno et al. 2010 excluded the alternative RG-II role. The plant end product is still unknown and Kdo-containing intermediates were not detected, but this does not undermine involvement in the lipid A precursor pathway. The low taxon rate-ratio reflected sparse plant curation of a minor, non-essential pathway, not absence of the pathway. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000602593 · WaaA/KdtA Kdo transferase ancestral node SUPPORTS TRANSFER AtKdtA is a single-copy full-length GT30 ortholog inside the clade that inherited the lipid A Kdo-transfer function; no evidence of divergence. UniProtKB:P0AC75 · E. coli WaaA (KdtA) SUPPORTS TRANSFER Biochemically characterised bifunctional Kdo transferase of the E. coli lipid A pathway; Arabidopsis kdta mutant chemistry matches the inherited role. Supporting Evidence: PMID:21709257 our work demonstrates that plants synthesize lipid A precursors using the same enzymatic pathway present in E. coli PMID:21709257 Lipid IV A ( Fig. 1 ) was detected only in the atkdta-1 mutant PMID:21709257 The disaccharide-1-phosphate intermediate generated by LpxB ( Fig. 1 ) accumulated in the atlpxk-1 and atkdta-1 mutants PMID:20124190 AtKDTA encodes a putative KDTA involved in the synthesis of a mitochondrial not yet identified lipid A-like molecule rather than in the synthesis of the cell wall RG-II |
| GO:0016020 membrane | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Membrane (is_active_in), propagated from the bacterial WaaA clade, where KdtA acts at the cytoplasmic face of the inner membrane on its membrane-embedded lipid substrate. Reason: The lipid acceptor (lipid IVA) is membrane-embedded, so membrane-associated activity is plausible and the family-level inference is reasonable. No experiment places AtKdtA in a particular mitochondrial membrane, so a more specific term (e.g. mitochondrial outer or inner membrane) is not supported; membrane is as precise as the evidence allows and is peripheral to the core annotation. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: PANTHER:PTN000602593 · WaaA/KdtA Kdo transferase ancestral node SUPPORTS TRANSFER Membrane association of the lipid-acceptor enzyme is a family trait; transfers defensibly to the mitochondrial plant enzyme. UniProtKB:P0AC75 · E. coli WaaA (KdtA) SUPPORTS TRANSFER E. coli WaaA acts on membrane-embedded lipid IVA at the inner membrane. Supporting Evidence: PMID:20124190 the fusion protein was demonstrated to be targeted to the mitochondria |
| GO:0016740 transferase activity | IBA GO_REF:0000033 | MODIFY | Summary: Transferase activity from PAINT node PTN000602593 (E. coli WaaA). Reason: Correct but very general. The specific activity inferred for the family and supported in Arabidopsis by lipid IVA accumulation in kdta mutants is Kdo transferase activity (GO:0043842), which the gene already carries via EC mapping. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000602593 · WaaA/KdtA Kdo transferase ancestral node SUPPORTS TRANSFER Node-level assertion is correct but less specific than the Kdo transferase activity the clade performs. UniProtKB:P0AC75 · E. coli WaaA (KdtA) SUPPORTS TRANSFER Source enzyme is a Kdo transferase; transferase activity is an uninformative ancestor. Proposed replacements: Kdo transferase activity Supporting Evidence: PMID:21709257 This step is followed by the transfer of two Kdo residues to lipid IV A by KdtA PMID:21709257 Lipid IV A ( Fig. 1 ) was detected only in the atkdta-1 mutant |
| GO:0016740 transferase activity | IEA GO_REF:0000002 | MODIFY | Summary: Transferase activity from InterPro2GO mapping of IPR039901 (Kdotransferase). Reason: Same claim as the IBA row; the InterPro entry itself is the Kdo transferase family, so the informative term is Kdo transferase activity (GO:0043842), already present on the gene. Proposed replacements: Kdo transferase activity Supporting Evidence: file:ARATH/KDTA/KDTA-uniprot.txt Belongs to the glycosyltransferase group 1 family. PMID:21709257 This step is followed by the transfer of two Kdo residues to lipid IV A by KdtA |
| GO:0036104 Kdo2-lipid A biosynthetic process | IEA GO_REF:0000041 | ACCEPT | Summary: Kdo2-lipid A biosynthetic process from UniPathway UPA00360 (steps 1 and 2 of Kdo2-lipid A from CMP-Kdo and lipid IV(A)). Reason: KdtA catalyses the Kdo transfer steps that define Kdo2-lipid A biosynthesis, and the UniProt pathway line rests on Li et al. 2011 (ECO:0000269). Caveat: the Arabidopsis end product has not been identified, and Kdo-lipid IVA and Kdo2-lipid IVA were below detection, so the structure of any plant Kdo2-lipid A-like molecule may differ from the E. coli molecule. The step-level assignment is still the best-supported description of the enzyme role. Supporting Evidence: file:ARATH/KDTA/KDTA-uniprot.txt lipid A from CMP-3-deoxy-D-manno-octulosonate and lipid IV(A): step PMID:21709257 This step is followed by the transfer of two Kdo residues to lipid IV A by KdtA PMID:21709257 Lipid IV A ( Fig. 1 ) was detected only in the atkdta-1 mutant PMID:21709257 We were unable to detect Kdo-lipid IV A , Kdo 2 -lipid IV A , and putative penta- or hexa-acylated derivatives |
| GO:0043842 Kdo transferase activity | IEA GO_REF:0000003 | ACCEPT | Summary: Kdo transferase activity from EC 2.4.99.12/2.4.99.13 mapping. Reason: Core molecular function. Supported by orthology to the biochemically characterised bifunctional E. coli KdtA (GT30 family, Pfam Glycos_transf_N) and by in planta genetics: loss of AtKdtA causes accumulation of its predicted acceptor, lipid IVA. No in vitro assay or E. coli complementation of AtKdtA has been reported, so the activity remains inferred rather than directly demonstrated (hence "probable" in UniProt). Supporting Evidence: PMID:21709257 Single copy genes encoding AtLpxB (AT2G04560), AtLpxK (AT3G20480) and AtKdtA (AT5G03770) ( Table 1 ) were also found, with 31, 26, and 34% sequence identity to the corresponding E. coli proteins, respectively PMID:21709257 Lipid IV A ( Fig. 1 ) was detected only in the atkdta-1 mutant PMID:21709257 This step is followed by the transfer of two Kdo residues to lipid IV A by KdtA |
Loading supporting content…
Download this section (compressed HTML)Q: Does recombinant AtKdtA transfer one or two Kdo residues to lipid IVA in vitro (mono- versus bifunctional), given that Kdo-lipid IVA and Kdo2-lipid IVA were not detected in planta?
Q: What is the final structure of the plant lipid A-like molecule downstream of KdtA, given that LpxL/LpxM orthologs are absent from Arabidopsis?
Q: Where does AtKdtA sit within mitochondria (outer membrane, inner membrane or matrix face), and does the pathway product reach chloroplast membranes?
Experiment: Express mature AtKdtA (without transit peptide), assay with lipid IVA and CMP-Kdo and identify products by LC-ESI/MS; complement an E. coli waaA (kdtA) depletion strain.
Hypothesis: AtKdtA is a bifunctional Kdo transferase that adds two Kdo residues to lipid IVA using CMP-Kdo.
Type: in vitro enzyme assay
Experiment: Protease protection and carbonate extraction of isolated mitochondria from tagged KDTA lines to place the enzyme at the outer or inner membrane.
Hypothesis: AtKdtA is membrane-associated in mitochondria, where its lipid substrate resides.
Type: sub-mitochondrial fractionation
Experiment: Challenge kdta null mutants with bacterial pathogens and mitochondrial stressors, and profile Kdo-containing lipids by targeted MS in isolated mitochondria.
Hypothesis: The plant lipid A-like product has a conditional role in mitochondrial membrane function or defence signalling.
Type: stress and pathogen phenotyping
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)