PASTICCINO2 (PAS2; also PEPINO, At5g10480) is the very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase (HCD) of the endoplasmic reticulum fatty acid elongase in Arabidopsis, the plant ortholog of yeast PHS1 and animal HACD/PTPLA proteins. It is a multi-pass integral ER membrane protein that catalyzes the third step of each very-long-chain fatty acid (VLCFA) elongation cycle, dehydrating the 3-hydroxyacyl-CoA produced by KCR1 to a trans-2,3-enoyl-CoA that is reduced by ECR/CER10, with which PAS2 physically associates. PAS2 is encoded by a single functional gene, is essential (null alleles are embryo lethal) and is rate-limiting for VLCFA production; hypomorphic pas2 mutants accumulate 3-hydroxyacyl-CoA intermediates, have reduced VLCFAs in seed triacylglycerols, cuticular waxes and sphingolipids, and show fused organs and ectopic, cytokinin-enhanced cell proliferation. Despite its historical classification as a protein tyrosine phosphatase-like protein, PAS2 carries a degenerate PTP motif and lacks phosphatase activity; an interaction with Tyr-phosphorylated CDKA;1 has been reported, but its developmental phenotypes are complemented by the yeast dehydratase and are largely attributable to VLCFA deficiency.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004725 protein tyrosine phosphatase activity | ISS PMID:12472687 Pasticcino2 is a protein tyrosine phosphatase-like involved ... | REMOVE | Summary: Assigned by sequence similarity to protein tyrosine phosphatases (the PTPL family). Reason: PAS2 belongs to the PTP-like (PTPLA/HACD) family defined by a mutated, non-catalytic PTP active site; recombinant PAS2 has no phosphatase activity, and the conserved catalytic residues of the family serve 3-hydroxyacyl-CoA dehydratase activity, not the PTP motif. The ISS phosphatase annotation is contradicted. Supporting Evidence: PMID:12472687 characterized by a mutated PTP active site PMID:16698944 The recombinant PAS2 had no phosphatase activity PMID:18799749 recent structure/function analysis of Phs1p identified the catalytic residues involved in the dehydratase activity, and they do not belong to the PTP motif file:ARATH/PAS2/PAS2-deep-research-falcon.md its primary experimentally validated function is dehydratase activity rather than phosphatase activity |
| GO:0005515 protein binding | IPI PMID:30604175 Arabidopsis Bax inhibitor-1 interacts with enzymes related t... | REMOVE | Summary: Interaction/co-purification of PAS2 with AtELO2, cytochrome b5 isoforms and AtBI-1. Reason: Generic 'protein binding' is uninformative. The interactions reflect PAS2's membership in the ER elongase assembly, which is captured by the fatty acid elongase complex and dehydratase activity annotations; 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. |
| GO:0005634 nucleus | IDA PMID:16698944 Arabidopsis PASTICCINO2 is an antiphosphatase involved in re... | MARK AS OVER ANNOTATED | Summary: Overexpressed 35S-PAS2:GFP showed nuclear as well as cytosolic signal in differentiated root cells and occasionally in BY-2 nuclei. Reason: The cached full text was read. The nuclear signal is a genuine observation, but it comes from a 35S-driven C-terminal GFP fusion in lines selected for high GFP that showed overexpression phenotypes, and in dividing cells the same fusion was principally excluded from the nucleus with perinuclear accumulation. PAS2 is a multi-pass integral ER membrane 3-hydroxyacyl-CoA dehydratase (like yeast Phs1p), and later work by the same group with a PAS2-GFP fusion found it mainly on the ER, co-localizing with the ER enoyl-CoA reductase CER10. The perinuclear signal fits the nuclear envelope/ER, and the nucleoplasmic signal in differentiated cells is most plausibly an overexpression or fusion-processing artefact. Neither paper establishes that a nuclear pool does any work. The row is marked as an over-annotation rather than removed because the authors did record nuclear GFP signal; ER membrane is the supported location. Supporting Evidence: PMID:16698944 most of the cells in the differentiated zone displayed cytosolic but also nuclear distribution of the PAS2:GFP protein fusion PMID:16698944 PAS2:GFP fusion protein was mainly found outside the nucleus with a strong accumulation in the perinuclear region PMID:16698944 High GFP-producing plants were retained for further analysis PMID:18799749 PAS2-GFP protein fusion was mainly associated with the ER and colocalized with CER10-mRFP1 |
| GO:0005634 nucleus | IEA GO_REF:0000044 | MARK AS OVER ANNOTATED | Summary: UniProt subcellular-location mapping (Nucleus), derived from the 35S-PAS2:GFP study. Reason: UniProt's Nucleus subcellular-location statement derives from the same 35S-PAS2:GFP study, so this electronic row makes the same claim as the IDA row and gets the same action. The supported location of this multi-pass ER enzyme is the ER membrane; nuclear signal of an overexpressed fusion is not good evidence of a functional nuclear pool. Supporting Evidence: PMID:16698944 most of the cells in the differentiated zone displayed cytosolic but also nuclear distribution of the PAS2:GFP protein fusion PMID:18799749 PAS2-GFP protein fusion was mainly associated with the ER and colocalized with CER10-mRFP1 |
| GO:0005737 cytoplasm | EXP PMID:16698944 Arabidopsis PASTICCINO2 is an antiphosphatase involved in re... | ACCEPT | Summary: PAS2:GFP localized outside the nucleus (cytoplasm) in dividing cells. Reason: Correct at a general level: the ER is part of the cytoplasm, and PAS2 is an ER membrane protein; the informative location is the ER membrane. Supporting Evidence: PMID:16698944 PAS2:GFP fusion protein was mainly found outside the nucleus with a strong accumulation in the perinuclear region PMID:18799749 PAS2-GFP protein fusion was mainly associated with the ER and colocalized with CER10-mRFP1 |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping (Cytoplasm). Reason: Correct but general; ER membrane is the informative location. |
| GO:0005739 mitochondrion | ISM GO_REF:0000122 | REMOVE | Summary: AtSubP sequence-based prediction of mitochondrion. Reason: Contradicted by experimental ER localization and ER-specific interaction with CER10; no evidence for mitochondrial PAS2. Supporting Evidence: PMID:18799749 PAS2-GFP protein fusion was mainly associated with the ER and colocalized with CER10-mRFP1 PMID:18799749 PAS2 was specifically associated in the endoplasmic reticulum with the enoyl-CoA reductase CER10, the fourth enzyme of the elongase complex |
| GO:0005783 endoplasmic reticulum | HDA PMID:22923678 Putative glycosyltransferases and other plant Golgi apparatu... | ACCEPT | Summary: LOPIT proteomics assigned PAS2 to the ER. Reason: Consistent with focused localization. Supporting Evidence: PMID:22923678 we identified the subcellular localization of 1,110 proteins with high confidence PMID:18799749 PAS2-GFP protein fusion was mainly associated with the ER and colocalized with CER10-mRFP1 |
| GO:0005789 endoplasmic reticulum membrane | EXP PMID:18799749 The very-long-chain hydroxy fatty acyl-CoA dehydratase PASTI... | ACCEPT | Summary: Native-promoter PAS2-GFP localizes to the ER and co-localizes with CER10-mRFP1; BiFC shows PAS2-CER10 interaction in the ER. Reason: Core localization of this multi-pass ER membrane dehydratase. Supporting Evidence: PMID:18799749 PAS2-GFP protein fusion was mainly associated with the ER and colocalized with CER10-mRFP1 PMID:18799749 PAS2 was specifically associated in the endoplasmic reticulum with the enoyl-CoA reductase CER10, the fourth enzyme of the elongase complex |
| GO:0005789 endoplasmic reticulum membrane | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference of ER membrane activity for the HACD/PHS1 clade (PTN000112207), with PAS2 among the experimentally characterized members. Reason: Correct; conserved from yeast Phs1p to plant PAS2. Supporting Evidence: PMID:18799749 PAS2-GFP protein fusion was mainly associated with the ER and colocalized with CER10-mRFP1 |
| GO:0005789 endoplasmic reticulum membrane | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping to ER membrane. Reason: Correct. |
| GO:0005829 cytosol | IDA PMID:16698944 Arabidopsis PASTICCINO2 is an antiphosphatase involved in re... | MARK AS OVER ANNOTATED | Summary: Overexpressed PAS2:GFP gave diffuse cytosolic signal in differentiated root cells. Reason: PAS2 is an integral multi-pass ER membrane protein; a soluble cytosolic pool is not supported by native-promoter localization, and diffuse signal from a strongly overexpressed C-terminal GFP fusion is not reliable evidence for cytosolic residence. Supporting Evidence: PMID:16698944 most of the cells in the differentiated zone displayed cytosolic but also nuclear distribution of the PAS2:GFP protein fusion PMID:18799749 PAS2-GFP protein fusion was mainly associated with the ER and colocalized with CER10-mRFP1 |
| 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:0009923 fatty acid elongase complex | IPI PMID:18799749 The very-long-chain hydroxy fatty acyl-CoA dehydratase PASTI... | ACCEPT | Summary: BiFC shows PAS2 interacts specifically with ECR/CER10 in the ER; PAS2 is the dehydratase subunit of the elongase. Reason: PAS2 is the sole HCD of the microsomal elongase and physically associates with the ECR subunit. Supporting Evidence: PMID:18799749 PAS2 was specifically associated in the endoplasmic reticulum with the enoyl-CoA reductase CER10, the fourth enzyme of the elongase complex |
| GO:0018812 3-hydroxyacyl-CoA dehydratase activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference of 3-hydroxyacyl-CoA dehydratase activity for the PHS1/HACD clade. Reason: Correct; the more specific very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase activity (GO:0102158) is used as the core function. Supporting Evidence: PMID:18799749 the defective elongation cycle resulted in the accumulation of 3-hydroxy-acyl-CoA intermediates, indicating premature termination of fatty acid elongation and confirming the role of PAS2 in this process |
| GO:0018812 3-hydroxyacyl-CoA dehydratase activity | IGI PMID:18799749 The very-long-chain hydroxy fatty acyl-CoA dehydratase PASTI... | ACCEPT | Summary: Reciprocal complementation between PAS2 and yeast PHS1 and accumulation of 3-hydroxyacyl-CoAs in pas2-1 establish PAS2 as the elongase dehydratase. Reason: Core activity supported by genetic and biochemical (acyl-CoA profiling) evidence. Supporting Evidence: PMID:18799749 the defective elongation cycle resulted in the accumulation of 3-hydroxy-acyl-CoA intermediates, indicating premature termination of fatty acid elongation and confirming the role of PAS2 in this process PMID:18799749 was able to restore phs1 cytokinesis defects and sphingolipid long chain base overaccumulation |
| GO:0030148 sphingolipid biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference that PHS1/HACD family members function in sphingolipid biosynthesis. Reason: PAS2 supplies the VLCFA moieties of ceramides and complex sphingolipids; pas2 mutants lose VLCFAs from glucosylceramides and accumulate free long-chain bases, which is rescued by PHS1. Supporting Evidence: PMID:18799749 The glucosylceramide pool showed an almost complete absence of VLCFAs PMID:18799749 was able to restore phs1 cytokinesis defects and sphingolipid long chain base overaccumulation |
| GO:0030154 cell differentiation | IMP PMID:9449673 The PASTICCINO genes of Arabidopsis thaliana are involved in... | KEEP AS NON CORE | Summary: pas2 mutants show uncoordinated, cytokinin-enhanced cell division and dedifferentiation. Reason: The developmental phenotype is a downstream consequence of defective VLCFA synthesis (it is complemented by the yeast dehydratase PHS1), not a direct role of PAS2 in a differentiation program. Supporting Evidence: PMID:9449673 They display uncoordinated cell divisions which are enhanced by cytokinin. PMID:18799749 PHS1 complementation indicates that pas2 developmental defects are most likely caused by a defective dehydratase activity in the VLCFA microsomal elongase complex. |
| GO:0030497 fatty acid elongation | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference of involvement in fatty acid elongation. Reason: Correct; PAS2 catalyzes the third step of the elongation cycle. Supporting Evidence: PMID:18799749 the defective elongation cycle resulted in the accumulation of 3-hydroxy-acyl-CoA intermediates, indicating premature termination of fatty acid elongation and confirming the role of PAS2 in this process |
| GO:0042761 very long-chain fatty acid biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference of involvement in VLCFA biosynthesis. Reason: Core process. Supporting Evidence: PMID:18799749 the plant 3-hydroxy-acyl-CoA dehydratase PASTICCINO2 is an essential and limiting enzyme in VLCFA synthesis |
| GO:0042761 very long-chain fatty acid biosynthetic process | IMP PMID:18799749 The very-long-chain hydroxy fatty acyl-CoA dehydratase PASTI... | ACCEPT | Summary: pas2-1 has reduced VLCFAs in seed TAG, wax and sphingolipids and accumulates 3-hydroxyacyl-CoA intermediates. Reason: Core process. Supporting Evidence: PMID:18799749 characterized by a general reduction of VLCFA pools in seed storage triacylglycerols, cuticular waxes, and complex sphingolipids PMID:18799749 the defective elongation cycle resulted in the accumulation of 3-hydroxy-acyl-CoA intermediates, indicating premature termination of fatty acid elongation and confirming the role of PAS2 in this process |
| GO:0048640 negative regulation of developmental growth | IMP PMID:16698944 Arabidopsis PASTICCINO2 is an antiphosphatase involved in re... | MARK AS OVER ANNOTATED | Summary: Overexpression of PAS2 inhibits seedling growth and alters leaf development. Reason: An overexpression phenotype does not establish a normal regulatory role in developmental growth; the growth effects of PAS2 dosage are explained by its limiting role in VLCFA synthesis (ectopic PHS1 also perturbs leaf development). Supporting Evidence: PMID:16698944 overexpression of PAS2 slowed down cell division in suspension cell cultures at the G2-to-M transition and early mitosis and inhibited Arabidopsis seedling growth PMID:18799749 the plant 3-hydroxy-acyl-CoA dehydratase PASTICCINO2 is an essential and limiting enzyme in VLCFA synthesis |
| GO:0051302 regulation of cell division | IMP PMID:16698944 Arabidopsis PASTICCINO2 is an antiphosphatase involved in re... | KEEP AS NON CORE | Summary: PAS2 binds Tyr-phosphorylated CDKA;1, loss of PAS2 increases CDKA;1 activity, and overexpression delays mitosis, leading to an 'antiphosphatase' model. Reason: The effect on cell division is experimentally observed, but subsequent work showed that pas2 developmental defects are rescued by the yeast dehydratase PHS1, indicating they largely stem from defective VLCFA synthesis; retained as non-core pending direct evidence for a separable CDK-regulatory function. Supporting Evidence: PMID:16698944 Loss of the PAS2 function dephosphorylated Arabidopsis thaliana CDKA;1 and upregulated its kinase activity. PMID:18799749 PHS1 complementation indicates that pas2 developmental defects are most likely caused by a defective dehydratase activity in the VLCFA microsomal elongase complex. |
| GO:0102158 very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase activity | IEA GO_REF:0000120 | ACCEPT | Summary: EC 4.2.1.134 / RHEA mapping to very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase activity. Reason: Correct and the most specific description of PAS2's catalytic function. Supporting Evidence: PMID:18799749 the defective elongation cycle resulted in the accumulation of 3-hydroxy-acyl-CoA intermediates, indicating premature termination of fatty acid elongation and confirming the role of PAS2 in this process |
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Download this section (compressed HTML)Q: Is the reported binding of PAS2 to Tyr15-phosphorylated CDKA;1 physiologically relevant, or are all cell-cycle phenotypes of pas2 secondary to altered VLCFA/sphingolipid homeostasis?
Q: Does the paralog At5g59770 (which cannot rescue yeast phs1) retain any dehydratase activity or partner with specific KCS isoforms?
Experiment: Express a catalytically dead PAS2 (mutating the residues equivalent to yeast Phs1p Y149/E152) in pas2 to test whether any developmental or CDKA;1-related phenotype is rescued independently of dehydratase activity.
Experiment: Determine PAS2 localization with a native-promoter, internally tagged functional fusion and immunogold/fractionation to resolve the reported nuclear pool.
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