CUT1 (also known as CER6/KCS6; At1g68530) is a 3-ketoacyl-CoA synthase (KCS; condensing enzyme) of the endoplasmic reticulum fatty acid elongase in Arabidopsis. It catalyzes the first and chain-length-determining step of each very-long-chain fatty acid (VLCFA) elongation cycle, condensing a very-long-chain acyl-CoA with malonyl-CoA to form a 3-oxoacyl-CoA; the reduction, dehydration and second reduction steps are performed by the shared elongase partners KCR1, PAS2 and ECR/CER10. CUT1 is an integral multi-pass ER membrane protein that acts on acyl-CoAs of C22 and longer, supplying the C26-C28+ VLCFA precursors that are converted into cuticular wax alkanes, ketones, alcohols and wax esters and into the long-chain lipids of the pollen coat. The gene is expressed almost exclusively in the epidermis of aerial organs and in the anther tapetum, and its transcription is light-dependent and enhanced by osmotic stress and abscisic acid. Loss or suppression of CUT1 produces a severely waxless (eceriferum) stem and silique surface and conditional male sterility caused by defective pollen-coat lipids and pollen hydration, while epidermis-driven overexpression increases stem wax load.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000038 very long-chain fatty acid metabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic (PAINT) inference that the plant FAE1-type KCS clade functions in VLCFA metabolism. CUT1 (AT1G68530) is itself among the experimentally characterized members seeding the node, which is expected, not circular. Reason: CUT1 is a bona fide member of the FAE1-like KCS family and its condensing activity is required for production of C24+ VLCFAs; the IBA is correctly placed and at an appropriate (if somewhat general) level. Supporting Evidence: PMID:10330468 In CUT1-suppressed plants, the C24 chain-length wax components predominate, suggesting that CUT1 is required for elongation of C24 VLCFAs. PMID:36798704 KCS5 and KCS6, which share 88% identity, led to the elongation of C22 into C24 up to C28 compounds |
| GO:0000038 very long-chain fatty acid metabolic process | IDA PMID:10330468 CUT1, an Arabidopsis gene required for cuticular wax biosynt... | ACCEPT | Summary: Millar et al. (1999) cloned CUT1 and showed that its suppression depletes VLCFA-derived stem wax, with C24 products accumulating, establishing a role in VLCFA elongation/metabolism. Reason: Consistent with CUT1 being a VLCFA condensing enzyme; the full text (not cached) was read by the curator. The more specific VLCFA biosynthetic/elongation role is the core process. Supporting Evidence: PMID:10330468 This result indicates that CUT1 is involved in the production of VLCFA precursors used for the synthesis of all stem wax components in Arabidopsis. |
| GO:0005737 cytoplasm | ISM GO_REF:0000122 | MARK AS OVER ANNOTATED | Summary: AtSubP sequence-based prediction of cytoplasm. Reason: Not strictly wrong (the ER lies within the cytoplasm), but CUT1 is an integral ER membrane protein and the uninformative cytoplasm call adds nothing beyond the experimentally supported ER membrane localization; it risks being read as a soluble cytosolic localization. Supporting Evidence: PMID:18465198 The analysis of the subcellular localization in tobacco cells of the different subunits of the acyl-CoA elongase shows that all these proteins are localized in the endoplasmic reticulum demonstrating that VLCFA production occurs in this compartment. |
| GO:0005739 mitochondrion | HDA PMID:28887381 Global Analysis of Membrane-associated Protein Oligomerizati... | MARK AS OVER ANNOTATED | Summary: High-throughput protein correlation profiling (size-exclusion chromatography of detergent-solubilized leaf membranes) assigned CUT1 to a mitochondrial fraction. Reason: This is a large-scale proteomics assignment, not a CUT1-focused study, and the paper text does not discuss CUT1. All focused studies place CUT1 and the other elongase subunits in the ER, so a mitochondrial call most likely reflects co-fractionation of ER membranes rather than steady-state residence. 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:36798704 The 21 Arabidopsis KCSs localize in the endoplasmic reticulum of tobacco cells. |
| GO:0005783 endoplasmic reticulum | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference of ER activity across the FAE1-type KCS clade, consistent with direct localization of all 21 Arabidopsis KCSs to the ER. Reason: Correct; VLCFA elongation takes place on the ER and CUT1 has been directly localized there. Supporting Evidence: PMID:36798704 The 21 Arabidopsis KCSs localize in the endoplasmic reticulum of tobacco cells. |
| GO:0005783 endoplasmic reticulum | IDA PMID:18465198 The VLCFA elongase gene family in Arabidopsis thaliana: phyl... | ACCEPT | Summary: Joubes et al. (2008) localized fluorescent-tagged elongase subunits, including the KCSs, to the ER in tobacco cells. Reason: Direct localization evidence consistent with the known site of VLCFA elongation. Supporting Evidence: PMID:18465198 The analysis of the subcellular localization in tobacco cells of the different subunits of the acyl-CoA elongase shows that all these proteins are localized in the endoplasmic reticulum demonstrating that VLCFA production occurs in this compartment. |
| GO:0005783 endoplasmic reticulum | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA machine-learning rule assigns ER localization. Reason: Correct and corroborated by direct localization data. Supporting Evidence: PMID:36798704 The 21 Arabidopsis KCSs localize in the endoplasmic reticulum of tobacco cells. |
| GO:0005789 endoplasmic reticulum membrane | EXP PMID:12467640 Biosynthesis and secretion of plant cuticular wax. | ACCEPT | Summary: ER membrane localization attributed to the Kunst and Samuels (2003) review of wax biosynthesis, which discusses FAE on the ER. Reason: The localization is correct (CUT1 is a multi-pass ER membrane protein) and is independently supported by primary localization data; the cited source is a review whose full text is not cached, so the EXP code is deferred to the curator. Supporting Evidence: PMID:12467640 Two hypotheses are presented for intracellular wax transport: direct transfer of lipids from the endoplasmic reticulum to the plasma membrane, and Golgi mediated exocytosis. PMID:36798704 The 21 Arabidopsis KCSs localize in the endoplasmic reticulum of tobacco cells. |
| GO:0005789 endoplasmic reticulum membrane | EXP PMID:18465198 The VLCFA elongase gene family in Arabidopsis thaliana: phyl... | ACCEPT | Summary: ER localization of elongase subunits in tobacco cells; CUT1 is predicted to be a multi-pass membrane protein, so the ER membrane is the appropriate component. Reason: Core localization. Supporting Evidence: PMID:18465198 all these proteins are localized in the endoplasmic reticulum demonstrating that VLCFA production occurs in this compartment |
| GO:0005789 endoplasmic reticulum membrane | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping (ER membrane; multi-pass). Reason: Correct, consistent with experimental evidence. |
| GO:0006633 fatty acid biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic mapping from KCS InterPro domains/UniPathway to fatty acid biosynthesis. Reason: Correct but general; the specific core process is VLCFA biosynthesis/elongation. |
| GO:0009409 response to cold | IEP PMID:18465198 The VLCFA elongase gene family in Arabidopsis thaliana: phyl... | KEEP AS NON CORE | Summary: Expression profiling of the elongase genes under stress; UniProt reports CER6 transcript down-regulated by low temperature in this study. Reason: Transcriptional responsiveness to cold is an expression-based (IEP) observation and a regulatory context for wax production, not the enzymatic function of CUT1. Supporting Evidence: PMID:18465198 The expression patterns in Arabidopsis of the acyl-CoA elongase genes suggest several levels of regulations at the tissular or organ level but also under stress conditions |
| GO:0009409 response to cold | IEP PMID:41718707 Transcription factor bZIP48-MYB96 module positively regulate... | KEEP AS NON CORE | Summary: Liu et al. (2026) report that cold stress induces wax biosynthesis through bZIP48-MYB96-mediated upregulation of KCS genes, enhancing freezing tolerance. Reason: Cold-induced wax deposition is a plausible physiological context for CUT1, but the evidence is transcriptional induction (abstract only; the specific KCSs are not named in the abstract), and the role is downstream of CUT1's condensing activity. Retained as non-core. Supporting Evidence: PMID:41718707 we reveal that wax biosynthesis in Arabidopsis is induced by cold stress, which is due to the significant upregulation of wax synthesis genes Ξ²-ketoacyl-CoA synthases (KCSs) and ECERIFERUMs (CERs) under cold stress |
| GO:0009416 response to light stimulus | IEP PMID:18465198 The VLCFA elongase gene family in Arabidopsis thaliana: phyl... | KEEP AS NON CORE | Summary: CER6/CUT1 transcription is light-dependent (down-regulated by darkness). Reason: Light-dependence of CER6 transcription is well documented (also by Hooker et al. 2002) and is a regulatory feature rather than a core function. Supporting Evidence: PMID:12177469 Our results demonstrate that light is essential for CER6 transcription, and that osmotic stress and the presence of abscisic acid enhance CER6 transcript accumulation. |
| GO:0009826 unidimensional cell growth | IMP PMID:17993622 Saturated very-long-chain fatty acids promote cotton fiber a... | KEEP AS NON CORE | Summary: Qin et al. (2007) showed that the dwarf stature and reduced stem cell length of the Arabidopsis cut1 mutant are rescued by exogenous C24:0 or a cotton CER6 homolog, proposing that saturated VLCFAs promote cell elongation via ethylene. Reason: The effect on cell elongation is an indirect, downstream consequence of VLCFA supply (proposed to act through ethylene signalling), not a direct activity of CUT1 in cell growth. Supporting Evidence: PMID:17993622 Wild-type architecture (leaf size and mature stem length) was observed in the Arabidopsis cut1 mutant when C24:0 was applied exogenously through the root system or when Gh KCS13 / CER6 , a homolog of Arabidopsis CER6 ( CUT1 ), was transformed into the cut1 mutant background |
| GO:0009922 fatty acid elongase activity | EXP PMID:10330468 CUT1, an Arabidopsis gene required for cuticular wax biosynt... | ACCEPT | Summary: GO:0009922 is defined as the condensation step (very-long-chain acyl-CoA + malonyl-CoA -> 3-oxoacyl-CoA + CO2 + CoA) of the ER elongation cycle, which is exactly the KCS activity of CUT1. Reason: Core molecular function. CUT1 encodes a VLCFA condensing enzyme required for C24+ elongation; yeast expression confirms elongation of C22 to C24-C28. Supporting Evidence: PMID:10330468 we have identified a gene, designated CUT1, that encodes a VLCFA condensing enzyme required for cuticular wax production PMID:36798704 KCS5 and KCS6, which share 88% identity, led to the elongation of C22 into C24 up to C28 compounds |
| GO:0009922 fatty acid elongase activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference of condensing (fatty acid elongase) activity for the plant KCS clade; CUT1 is among the experimentally characterized descendants. Reason: Correct node placement; CUT1 retains the catalytic KCS domains and has experimentally demonstrated condensing activity. Supporting Evidence: PMID:36798704 KCS5 and KCS6, which share 88% identity, led to the elongation of C22 into C24 up to C28 compounds |
| GO:0009922 fatty acid elongase activity | IEA GO_REF:0000120 | ACCEPT | Summary: EC 2.3.1.199 / RHEA:32727 mapping to fatty acid elongase (condensing) activity. Reason: Correct mapping for a very-long-chain 3-oxoacyl-CoA synthase. |
| GO:0010025 wax biosynthetic process | IMP PMID:10330468 CUT1, an Arabidopsis gene required for cuticular wax biosynt... | ACCEPT | Summary: CUT1 sense suppression reduces stem wax to 6-7% of wild type and removes all wax crystals, affecting both the decarbonylation and acyl-reduction branches. Reason: CUT1 catalyzes the condensation step producing the C26+ VLCFA precursors of all stem wax classes; wax biosynthesis is the principal physiological process it serves. Participation is direct (it catalyzes a step producing the wax precursor pool). Supporting Evidence: PMID:10330468 chemical analyses of waxless plants demonstrated that the stem wax load was reduced to 6 to 7% of wild-type levels PMID:12177469 these data implicate CER6 as the major condensing enzyme for stem wax and pollen coat lipid biosynthesis |
| GO:0016020 membrane | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO membrane assignment. Reason: Correct but general; the informative location is the ER membrane. |
| GO:0016746 acyltransferase activity | IEA GO_REF:0000002 | ACCEPT | Summary: Thiolase-like superfamily domain maps to acyltransferase activity. Reason: Correct but general parent of the condensing (fatty acid elongase) activity. |
| GO:0016747 acyltransferase activity, transferring groups other than amino-acyl groups | IEA GO_REF:0000002 | ACCEPT | Summary: KCS domain maps to acyltransferase (non-aminoacyl) activity, the direct parent of fatty acid elongase activity. Reason: Correct but general; GO:0009922 is the informative term. |
| GO:0160062 cutin-based cuticle development | IDA PMID:10330468 CUT1, an Arabidopsis gene required for cuticular wax biosynt... | KEEP AS NON CORE | Summary: CUT1-suppressed plants lack epicuticular wax crystals, so CUT1 contributes to formation of the cuticle (via its wax component). Reason: CUT1 contributes VLCFA precursors to cuticular wax, a component of the cuticle; its role in cuticle development is real but indirect relative to its core wax/VLCFA biosynthetic role. Supporting Evidence: PMID:10330468 Scanning electron microscopy revealed that this was a severe waxless phenotype, because stems of CUT1-suppressed plants were completely devoid of wax crystals. |
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Download this section (compressed HTML)Q: What structural features of CUT1/KCS6 confine it to C22+ acyl-CoA substrates, and how do the non-catalytic CER2-LIKE (BAHD-like) proteins extend its product range beyond C28?
Q: Does CUT1 form distinct elongase complexes with KCR1, PAS2 and ECR in the epidermis versus the tapetum, and does complex composition affect product chain length for wax versus pollen-coat lipids?
Experiment: In vitro reconstitution of CUT1 with purified KCR1, PAS2 and ECR in proteoliposomes, with and without CER2/CER2-LIKE proteins, to quantify chain-length product profiles and kinetic parameters on C22-C28 acyl-CoA substrates.
Experiment: Cell-type-specific complementation of cut1/cer6 using epidermis- versus tapetum-specific promoters to separate the cuticular wax and pollen-coat (fertility) functions.
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