KCR1 (beta-ketoacyl-CoA reductase 1; also GLOSSY8-like, At1g67730) is the 3-ketoacyl-CoA reductase of the endoplasmic reticulum fatty acid elongase in Arabidopsis. It is a short-chain dehydrogenase/reductase family enzyme anchored in the ER membrane by an N-terminal transmembrane segment and retained there by a C-terminal dilysine motif. KCR1 catalyzes the second step of each very-long-chain fatty acid (VLCFA) elongation cycle, the NAD(P)H-dependent reduction of the 3-ketoacyl-CoA produced by a condensing enzyme (KCS) to a (3R)-3-hydroxyacyl-CoA, which is then dehydrated by PAS2 and reduced by ECR/CER10. Unlike the many substrate-specific KCS isoforms, KCR1 is a shared, broadly expressed core subunit and is the only functional microsomal KCR in Arabidopsis (the paralog KCR2 is inactive). Consequently it supplies VLCFAs for sphingolipids, seed triacylglycerols, cuticular waxes, suberin and root glycerolipids; loss of KCR1 is embryo lethal, and partial suppression causes organ fusion, reduced wax load and altered VLCFA composition of multiple lipid classes.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005515 protein binding | IPI PMID:30604175 Arabidopsis Bax inhibitor-1 interacts with enzymes related t... | REMOVE | Summary: Co-immunoprecipitation/mass spectrometry and interaction assays showed KCR1 associating with AtELO2, cytochrome b5 isoforms and the cell-death regulator AtBI-1 in an ER complex. Reason: Generic 'protein binding' conveys no functional information. The reported interactions (with AtELO2/AtCb5/AtBI-1) are consistent with KCR1 acting within the ER elongase assembly, which is better captured by the specific reductase activity and ER membrane terms; removal does not dispute the interactions. Supporting Evidence: PMID:30604175 AtELO2 and AtCb5-B also interact with KCR1, PAS2, and CER10, which are essential for the synthesis of VLCFAs. PMID:30604175 AtBI-1 forms a complex with AtELO2, KCR1, PAS2, CER10, and AtCb5-D |
| GO:0005739 mitochondrion | HDA PMID:28887381 Global Analysis of Membrane-associated Protein Oligomerizati... | MARK AS OVER ANNOTATED | Summary: High-throughput protein correlation profiling assigned KCR1 to a mitochondrial fraction. Reason: Large-scale co-fractionation assignment not discussed in the paper text; focused imaging of a functional YFP-KCR1 fusion shows exclusive ER labelling, so the mitochondrial call most likely reflects co-migration of ER membranes. Supporting Evidence: PMID:28887381 Here we combined cell fractionation of Arabidopsis leaves with nondenaturing detergent solubilization and LC/MS-based profiling of size exclusion chromatography fractions to measure the apparent masses of >1350 membrane-associated proteins. PMID:19439572 In all the complemented YFP-AtKCR1 transgenic lines examined by confocal microscopy, YFP fluorescence labeled a reticulate network typical of the ER file:ARATH/KCR1/KCR1-deep-research-falcon.md no evidence supports mitochondrial localization |
| GO:0005783 endoplasmic reticulum | HDA PMID:16618929 Mapping the Arabidopsis organelle proteome. | ACCEPT | Summary: LOPIT organelle proteomics (Dunkley et al. 2006) assigned KCR1 to the ER. Reason: High-throughput, but fully consistent with focused localization of a functional fluorescent KCR1 fusion to the ER. Supporting Evidence: PMID:16618929 enabling confident and simultaneous localization of 527 proteins to the endoplasmic reticulum, Golgi apparatus, vacuolar membrane, plasma membrane, or mitochondria and plastids PMID:19439572 Fluorescent protein-tagged AtKCR1 and AtKCR2 were localized to the endoplasmic reticulum, the site of fatty acid elongation. |
| GO:0005783 endoplasmic reticulum | HDA PMID:22923678 Putative glycosyltransferases and other plant Golgi apparatu... | ACCEPT | Summary: LOPIT proteomics (Nikolovski et al. 2012) assigned KCR1 to the ER. Reason: Consistent with focused localization data. Supporting Evidence: PMID:22923678 we identified the subcellular localization of 1,110 proteins with high confidence PMID:19439572 Fluorescent protein-tagged AtKCR1 and AtKCR2 were localized to the endoplasmic reticulum, the site of fatty acid elongation. |
| GO:0005783 endoplasmic reticulum | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference of ER activity for the KCR clade (PTN001212488), with KCR1 among the experimentally characterized members. Reason: Correct; KCR1 is an ER-resident elongase subunit. The target appearing among the node's sources reflects its own experimental grounding. Supporting Evidence: PMID:19439572 Fluorescent protein-tagged AtKCR1 and AtKCR2 were localized to the endoplasmic reticulum, the site of fatty acid elongation. |
| GO:0005783 endoplasmic reticulum | IDA PMID:19439572 Functional characterization of the Arabidopsis beta-ketoacyl... | ACCEPT | Summary: A functional YFP-KCR1 fusion (complementing the embryo-lethal kcr1 mutant) labels a reticulate ER network in Arabidopsis. Reason: Direct localization with a demonstrably functional fusion protein. Supporting Evidence: PMID:19439572 In all the complemented YFP-AtKCR1 transgenic lines examined by confocal microscopy, YFP fluorescence labeled a reticulate network typical of the ER |
| GO:0005783 endoplasmic reticulum | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA rule assigning ER localization. Reason: Correct; corroborated experimentally. Supporting Evidence: PMID:19439572 Fluorescent protein-tagged AtKCR1 and AtKCR2 were localized to the endoplasmic reticulum, the site of fatty acid elongation. |
| GO:0005789 endoplasmic reticulum membrane | EXP PMID:19439572 Functional characterization of the Arabidopsis beta-ketoacyl... | ACCEPT | Summary: ER membrane localization; KCR1 has an N-terminal transmembrane segment and a C-terminal dilysine ER-retention motif. Reason: Core localization; the ER membrane is the site of microsomal fatty acid elongation. Supporting Evidence: PMID:19439572 Fluorescent protein-tagged AtKCR1 and AtKCR2 were localized to the endoplasmic reticulum, the site of fatty acid elongation. PMID:19439572 though a dilysine motif required for ER retention is obvious only in AtKCR1 |
| GO:0005789 endoplasmic reticulum membrane | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping to ER membrane. Reason: Correct, consistent with experimental data. |
| GO:0006633 fatty acid biosynthetic process | IEA GO_REF:0000041 | ACCEPT | Summary: UniPathway-based mapping to fatty acid biosynthesis. Reason: Correct but general; the informative process is VLCFA biosynthesis. |
| GO:0009507 chloroplast | ISM GO_REF:0000122 | REMOVE | Summary: AtSubP sequence-based prediction of chloroplast localization. Reason: Contradicted by direct localization of a functional KCR1 fusion to the ER; KCR1 carries an ER-retention dilysine motif and no plastid targeting evidence. Supporting Evidence: PMID:19439572 In all the complemented YFP-AtKCR1 transgenic lines examined by confocal microscopy, YFP fluorescence labeled a reticulate network typical of the ER |
| GO:0009793 embryo development ending in seed dormancy | IMP PMID:19439572 Functional characterization of the Arabidopsis beta-ketoacyl... | KEEP AS NON CORE | Summary: Homozygous kcr1 insertion mutants are embryo lethal, with embryos arresting at the globular stage; the defect is complemented by YFP-KCR1. Reason: The requirement for embryogenesis reflects the essential need for VLCFAs (e.g. for sphingolipids) rather than a developmental-regulatory role of KCR1; retained as a non-core phenotype-based process. Supporting Evidence: PMID:19439572 loss of AtKCR1 function results in embryo lethality, which cannot be rescued by AtKCR2 expression using the AtKCR1 promoter PMID:19439572 In contrast, embryos from white seeds arrested at the globular stage |
| GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA assignment of NAD(P)-dependent CH-OH oxidoreductase activity. Reason: Correct parent of the specific very-long-chain 3-oxoacyl-CoA reductase activity (GO:0141040). |
| GO:0018454 acetoacetyl-CoA reductase activity | IMP PMID:19439572 Functional characterization of the Arabidopsis beta-ketoacyl... | MODIFY | Summary: Annotated from the KCR1 study; GO:0018454 is the generic (R)-3-hydroxyacyl-CoA/3-oxoacyl-CoA NADPH reductase reaction. Reason: The activity is correct in essence, but KCR1 is the microsomal elongase beta-ketoacyl-CoA reductase acting on very-long-chain substrates; the specific term GO:0141040 (the second step of the ER elongation cycle) is the precise descriptor. Proposed replacements: very-long-chain 3-oxoacyl-CoA reductase activity Supporting Evidence: PMID:19439572 indicating that the Arabidopsis and yeast enzymes are functionally equivalent and that AtKCR1 also likely catalyzes the reduction of the Ξ² -ketoacyl-CoA PMID:19439572 these results indicate that only AtKCR1 is a functional KCR isoform involved in microsomal fatty acid elongation |
| GO:0042761 very long-chain fatty acid biosynthetic process | IMP PMID:19439572 Functional characterization of the Arabidopsis beta-ketoacyl... | ACCEPT | Summary: KCR1 RNAi lines have reduced cuticular wax and altered VLCFA composition of sphingolipids, seed TAGs and root glycerolipids. Reason: Core process: KCR1 catalyzes the second step of every VLCFA elongation cycle. Supporting Evidence: PMID:19439572 suppressed KCR activity results in a reduction of cuticular wax load and affects VLCFA composition of sphingolipids, seed triacylglycerols, and root glycerolipids, demonstrating in planta that KCR is involved in elongation reactions supplying VLCFA for all these diverse classes of lipids |
| GO:0045703 ketoreductase activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference of ketoreductase activity for the KCR clade (PTN001212488). Reason: Correct, though general; the node spans KCR1 and its divergent paralog KCR2, so a general term at this node is reasonable. For KCR1 the specific very-long-chain 3-oxoacyl-CoA reductase activity (GO:0141040) is separately supported by EXP and is used as the core function. Supporting Evidence: PMID:19439572 indicating that the Arabidopsis and yeast enzymes are functionally equivalent and that AtKCR1 also likely catalyzes the reduction of the Ξ² -ketoacyl-CoA |
| GO:0045703 ketoreductase activity | IDA PMID:11792704 A Saccharomyces cerevisiae gene required for heterologous fa... | ACCEPT | Summary: Beaudoin et al. (2002) showed that the Arabidopsis YBR159w homologue (At1g67730, KCR1) restores heterologous elongase activity in the yeast ybr159 mutant, whose microsomes are defective specifically in beta-ketoacyl reduction. Reason: Correct (if general) and supported by functional complementation; the specific very-long-chain 3-oxoacyl-CoA reductase activity (GO:0141040) is captured by the EXP annotation and used as the core function. Supporting Evidence: PMID:11792704 Both Ybr159p and an Arabidopsis homologue were shown to restore heterologous elongase activities when expressed in ybr159Delta mutants. PMID:11792704 Biochemical characterization of microsomal preparations from ybr159Delta cells revealed a primary perturbation in beta-ketoacyl reduction |
| GO:0141040 very-long-chain 3-oxoacyl-CoA reductase activity | EXP PMID:19439572 Functional characterization of the Arabidopsis beta-ketoacyl... | ACCEPT | Summary: Very-long-chain 3-oxoacyl-CoA reductase activity is supported by functional complementation of the yeast KCR mutant and in planta lipid phenotypes. Reason: Core molecular function of KCR1. Supporting Evidence: PMID:19439572 indicating that the Arabidopsis and yeast enzymes are functionally equivalent and that AtKCR1 also likely catalyzes the reduction of the Ξ² -ketoacyl-CoA PMID:19439572 these results indicate that only AtKCR1 is a functional KCR isoform involved in microsomal fatty acid elongation |
| GO:0141040 very-long-chain 3-oxoacyl-CoA reductase activity | IEA GO_REF:0000120 | ACCEPT | Summary: EC 1.1.1.330 / RHEA:48680 mapping. Reason: Correct mapping, consistent with experimental data. |
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Download this section (compressed HTML)Q: Does KCR1 abundance limit flux through the elongase when several KCS isoforms compete for it, as proposed to explain fiddlehead-like phenotypes without glossiness in KCR1-RNAi lines?
Q: Is KCR2 a pseudo-enzyme or does it reduce a non-VLCFA 3-oxo substrate, given that it lacks KCR activity in yeast yet is conserved and ER-localized?
Experiment: Assay NADH- versus NADPH-dependent reduction of C18-C28 3-oxoacyl-CoAs by purified or microsomal KCR1 (and KCR2) to define chain-length kinetics and test whether KCR2 retains any activity.
Experiment: Titrate KCR1 expression (inducible RNAi / overexpression) in lines expressing different KCS isoforms and measure acyl-CoA and 3-oxo/3-hydroxy intermediates to test whether KCR1 is rate-limiting for specific elongase complexes.
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