Farnesyl diphosphate synthase 1 (FPS1, At5g47770) of Arabidopsis thaliana is a Mg2+-dependent trans-prenyltransferase of the FPP/GGPP synthase family that catalyses the two successive head-to-tail condensations of isopentenyl diphosphate (IPP) with dimethylallyl diphosphate (DMAPP) and then with the resulting geranyl diphosphate (GPP), producing (2E,6E)-farnesyl diphosphate (FPP). FPP is the branch-point precursor of sterols and brassinosteroids, triterpenoids, sesquiterpenoids, polyprenols, the ubiquinone side chain and farnesylated proteins. Alternative translation initiation produces a cytosolic short isoform (FPS1S) and a long isoform (FPS1L) whose 41-residue N-terminal transit peptide targets it to mitochondria. FPS1 is broadly expressed and provides most FPS activity through the plant life cycle; it is functionally redundant with the cytosolic paralog FPS2, and loss of both genes arrests embryo development.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004161 dimethylallyltranstransferase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Dimethylallyltranstransferase (DMAPP + IPP -> GPP) is the first of the two condensations catalysed by FPS; inherited across the FPP synthase clade. Reason: The PAINT node PTN000162949 covers eukaryotic FPP synthases, with experimental seeds including FPS1 itself, FPS2, yeast ERG20 and mouse Fdps. FPS1 sits squarely inside this clade (FPP/GGPP synthase family, conserved DDxxD motifs) and the purified FPS1S enzyme uses DMAPP as allylic substrate, so the inherited first-step activity holds. Supporting Evidence: file:ARATH/FPS1/FPS1-uniprot.txt Belongs to the FPP/GGPP synthase family. PMID:23145086 Both enzymes displayed typical Michaelis-Menten behaviour, as observed for other FPSs, and exhibited similar K m values in the µmolar range (from 8.3 to 31.5 µM) for both IPP and the allylic substrates DMAPP and GPP. |
| GO:0004161 dimethylallyltranstransferase activity | IDA PMID:23145086 Characterization of Arabidopsis FPS isozymes and FPS gene ex... | ACCEPT | Summary: Purified recombinant FPS1S condenses IPP with DMAPP (Km measured for DMAPP), i.e. dimethylallyltranstransferase activity. Reason: Keim et al. purified FPS1S expressed in E. coli and determined steady-state kinetics with DMAPP and GPP as allylic substrates; the DMAPP-dependent reaction is the GPP-forming first condensation. Core activity. Supporting Evidence: PMID:23145086 Purified FPS1S and FPS2 were also subjected to kinetic analyses and the resulting steady-state kinetic constants are shown in Table 1. PMID:23145086 Both enzymes displayed typical Michaelis-Menten behaviour, as observed for other FPSs, and exhibited similar K m values in the µmolar range (from 8.3 to 31.5 µM) for both IPP and the allylic substrates DMAPP and GPP. |
| GO:0004161 dimethylallyltranstransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic mapping from EC 2.5.1.1/RHEA:22408; consistent with experimental data. Reason: Same claim as the IDA and IBA rows; FPS1 catalyses the DMAPP + IPP condensation (UniProt catalytic activity, Keim et al. kinetics). Supporting Evidence: file:ARATH/FPS1/FPS1-uniprot.txt Catalyzes the sequential condensation of isopentenyl pyrophosphate with the allylic pyrophosphates, dimethylallyl pyrophosphate, and then with the resultant geranylpyrophosphate to the ultimate product farnesyl pyrophosphate. PMID:23145086 Both enzymes displayed typical Michaelis-Menten behaviour, as observed for other FPSs, and exhibited similar K m values in the µmolar range (from 8.3 to 31.5 µM) for both IPP and the allylic substrates DMAPP and GPP. |
| GO:0004337 (2E,6E)-farnesyl diphosphate synthase activity | IBA GO_REF:0000033 | ACCEPT | Summary: (2E,6E)-farnesyl diphosphate synthase activity inherited from the eukaryotic FPS clade. Reason: FPS1 is a canonical member of the FPP synthase subfamily (PTHR11525:SF0) and the IBD is grounded in many experimentally characterised FPSs including FPS1 itself; target appearance among donors reflects its own IDA. Core activity. Supporting Evidence: file:ARATH/FPS1/FPS1-uniprot.txt Belongs to the FPP/GGPP synthase family. PMID:23145086 Both enzymes displayed typical Michaelis-Menten behaviour, as observed for other FPSs, and exhibited similar K m values in the µmolar range (from 8.3 to 31.5 µM) for both IPP and the allylic substrates DMAPP and GPP. |
| GO:0004337 (2E,6E)-farnesyl diphosphate synthase activity | IDA PMID:23145086 Characterization of Arabidopsis FPS isozymes and FPS gene ex... | ACCEPT | Summary: Purified FPS1S has FPP synthase activity (IPP + GPP -> FPP), with a preference for GPP over DMAPP. Reason: Direct biochemical characterisation of recombinant FPS1S (kinetics with GPP and IPP). This is the defining activity of the gene product; the cytosolic and mitochondrial isoforms share the identical catalytic domain. Supporting Evidence: PMID:23145086 Purified FPS1S and FPS2 were also subjected to kinetic analyses and the resulting steady-state kinetic constants are shown in Table 1. PMID:23145086 Both enzymes displayed typical Michaelis-Menten behaviour, as observed for other FPSs, and exhibited similar K m values in the µmolar range (from 8.3 to 31.5 µM) for both IPP and the allylic substrates DMAPP and GPP. |
| GO:0004337 (2E,6E)-farnesyl diphosphate synthase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic mapping from EC 2.5.1.10/RHEA:19361; consistent with experimental data. Reason: Same claim as the IDA/IBA rows. Supporting Evidence: file:ARATH/FPS1/FPS1-uniprot.txt Catalyzes the sequential condensation of isopentenyl pyrophosphate with the allylic pyrophosphates, dimethylallyl pyrophosphate, and then with the resultant geranylpyrophosphate to the ultimate product farnesyl pyrophosphate. PMID:23145086 Both enzymes displayed typical Michaelis-Menten behaviour, as observed for other FPSs, and exhibited similar K m values in the µmolar range (from 8.3 to 31.5 µM) for both IPP and the allylic substrates DMAPP and GPP. |
| GO:0004659 prenyltransferase activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO prenyltransferase activity; correct but a general parent of the specific FPS activities. Reason: GO:0004337 (2E,6E)-farnesyl diphosphate synthase activity is_a GO:0004659 prenyltransferase activity (checked with OAK); the specific activity is experimentally established for FPS1 and is already carried by the gene. Proposed replacements: (2E,6E)-farnesyl diphosphate synthase activity Supporting Evidence: PMID:23145086 Both enzymes displayed typical Michaelis-Menten behaviour, as observed for other FPSs, and exhibited similar K m values in the µmolar range (from 8.3 to 31.5 µM) for both IPP and the allylic substrates DMAPP and GPP. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | MODIFY | Summary: UniProt SubCell cytoplasm; true for the FPS1S isoform but less specific than the demonstrated cytosol location. Reason: GFP fusions of FPS1S show exclusive cytosolic, non-peroxisomal localization; GO:0005829 cytosol is part_of GO:0005737 (checked with OAK) and the gene already carries cytosol rows. Proposed replacements: cytosol Supporting Evidence: PMID:23145086 Under our experimental conditions all the four fusion proteins localized exclusively in the cytosol (Figure 5). |
| GO:0005737 cytoplasm | ISM GO_REF:0000122 | MODIFY | Summary: AtSubP prediction of cytoplasm; consistent with, but less specific than, experimental cytosol localization. Reason: As for the IEA cytoplasm row: refine to cytosol, which is demonstrated by GFP fusion localization of FPS1S. Proposed replacements: cytosol Supporting Evidence: PMID:23145086 Under our experimental conditions all the four fusion proteins localized exclusively in the cytosol (Figure 5). |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | ACCEPT | Summary: Mitochondrion, via UniProt SubCell; applies to the FPS1L isoform that carries a 41-residue mitochondrial transit peptide. Reason: The UniProt keyword rests on Cunillera et al. 1997, who showed the FPS1L N-terminal extension imports a passenger protein into yeast mitochondria and into purified plant mitochondria. The organelle claim holds. Only one line (the cleavable presequence/import assay) bears on the sub-compartment, so no matrix or membrane term is added. FPS1L supplies FPP for mitochondrial isoprenoids such as the ubiquinone side chain. Supporting Evidence: PMID:9182568 The functionality of the FPS1L NH2-terminal extension as a mitochondrial transit peptide was demonstrated by its ability to direct a passenger protein to yeast mitochondria in vivo and by in vitro import experiments using purified plant mitochondria. PMID:23145086 The FPS1 gene encodes FPS1S and FPS1L, which differ only by an N-terminal extension of 41 amino acid residues that targets FPS1L into mitochondria |
| GO:0005829 cytosol | HDA PMID:25293756 A proteomic strategy for global analysis of plant protein co... | ACCEPT | Summary: FPS1 detected in the crude cytosolic fraction of Arabidopsis leaves by size-exclusion/MS profiling. Reason: High-throughput detection agrees with targeted GFP localization of FPS1S to the cytosol. Supporting Evidence: PMID:25293756 Applying this approach to the crude cytosolic fraction of Arabidopsis thaliana leaves PMID:23145086 Under our experimental conditions all the four fusion proteins localized exclusively in the cytosol (Figure 5). |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: Cytosol as the site of activity, inherited from eukaryotic FPS orthologs. Reason: The cytosolic short isoform FPS1S is the predominant FPS1 product and GFP fusions are exclusively cytosolic; the inherited location holds. Supporting Evidence: PMID:23145086 Under our experimental conditions all the four fusion proteins localized exclusively in the cytosol (Figure 5). |
| GO:0008299 isoprenoid biosynthetic process | IEA GO_REF:0000002 | MODIFY | Summary: Isoprenoid biosynthetic process from InterPro; true but general. Reason: GO:0045337 trans,trans-farnesyl diphosphate biosynthetic process is_a GO:0008299 isoprenoid biosynthetic process (checked with OAK) and is the specific process FPS1 executes; the gene already carries it. Proposed replacements: trans, trans-farnesyl diphosphate biosynthetic process Supporting Evidence: file:ARATH/FPS1/FPS1-uniprot.txt Catalyzes the sequential condensation of isopentenyl pyrophosphate with the allylic pyrophosphates, dimethylallyl pyrophosphate, and then with the resultant geranylpyrophosphate to the ultimate product farnesyl pyrophosphate. PMID:23145086 Both enzymes displayed typical Michaelis-Menten behaviour, as observed for other FPSs, and exhibited similar K m values in the µmolar range (from 8.3 to 31.5 µM) for both IPP and the allylic substrates DMAPP and GPP. |
| GO:0009536 plastid | HDA PMID:28887381 Global Analysis of Membrane-associated Protein Oligomerizati... | MARK AS OVER ANNOTATED | Summary: Plastid, from a detergent-solubilised membrane-associated proteome of Arabidopsis leaves. Reason: FPS1 isoforms have no plastid targeting signal; FPS1S is exclusively cytosolic by GFP fusion and FPS1L is imported into mitochondria. The plastid assignment comes from a global co-fractionation dataset rather than a targeted assay, and plastidial prenyl diphosphate synthesis uses MEP-derived precursors and GGPPS/GPPS enzymes. Kept but flagged as not representative of FPS1 location. Supporting Evidence: PMID:23145086 Under our experimental conditions all the four fusion proteins localized exclusively in the cytosol (Figure 5). PMID:9182568 The functionality of the FPS1L NH2-terminal extension as a mitochondrial transit peptide was demonstrated by its ability to direct a passenger protein to yeast mitochondria in vivo and by in vitro import experiments using purified plant mitochondria. file:ARATH/FPS1/FPS1-deep-research-manual.md There is no plastid targeting signal and no targeted experiment supporting plastid localization. |
| GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO alkyl/aryl transferase activity; correct but very general. Reason: GO:0004337 is a descendant of GO:0016765 (checked with OAK); refine to the experimentally established FPP synthase activity. Proposed replacements: (2E,6E)-farnesyl diphosphate synthase activity Supporting Evidence: PMID:23145086 Both enzymes displayed typical Michaelis-Menten behaviour, as observed for other FPSs, and exhibited similar K m values in the µmolar range (from 8.3 to 31.5 µM) for both IPP and the allylic substrates DMAPP and GPP. |
| GO:0033384 geranyl diphosphate biosynthetic process | IEA GO_REF:0000041 | KEEP AS NON CORE | Summary: Geranyl diphosphate biosynthetic process via UniPathway; GPP is formed as the enzyme intermediate of the FPS reaction. Reason: FPS1 catalyses the DMAPP + IPP -> GPP condensation (accepted dimethylallyltranstransferase activity), so it does make GPP, but GPP is mainly an intermediate further elongated to FPP; free GPP for monoterpenes in plants comes from plastidial GPP synthases. True but peripheral to the FPP-producing core function. Supporting Evidence: file:ARATH/FPS1/FPS1-uniprot.txt Catalyzes the sequential condensation of isopentenyl pyrophosphate with the allylic pyrophosphates, dimethylallyl pyrophosphate, and then with the resultant geranylpyrophosphate to the ultimate product farnesyl pyrophosphate. |
| GO:0045337 trans, trans-farnesyl diphosphate biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: FPP biosynthetic process inherited across the FPS clade. Reason: FPS1 executes the final step of FPP synthesis; inherited process consistent with its own biochemistry. Supporting Evidence: file:ARATH/FPS1/FPS1-uniprot.txt Catalyzes the sequential condensation of isopentenyl pyrophosphate with the allylic pyrophosphates, dimethylallyl pyrophosphate, and then with the resultant geranylpyrophosphate to the ultimate product farnesyl pyrophosphate. PMID:23145086 Both enzymes displayed typical Michaelis-Menten behaviour, as observed for other FPSs, and exhibited similar K m values in the µmolar range (from 8.3 to 31.5 µM) for both IPP and the allylic substrates DMAPP and GPP. |
| GO:0045337 trans, trans-farnesyl diphosphate biosynthetic process | IDA PMID:23145086 Characterization of Arabidopsis FPS isozymes and FPS gene ex... | ACCEPT | Summary: FPP biosynthesis by purified FPS1S (acts_upstream_of_or_within). Reason: Purified FPS1S synthesises FPP from IPP and DMAPP/GPP; in planta FPS1 provides most FPS activity throughout the life cycle and one functional FPS gene suffices for FPP-derived isoprenoid synthesis. Supporting Evidence: PMID:23145086 Both enzymes displayed typical Michaelis-Menten behaviour, as observed for other FPSs, and exhibited similar K m values in the µmolar range (from 8.3 to 31.5 µM) for both IPP and the allylic substrates DMAPP and GPP. PMID:20497375 FPS1 activity has a predominant role during most of the plant life cycle, and FPS2 appears to have a major role in seeds and during the early stages of seedling development. |
| GO:0045337 trans, trans-farnesyl diphosphate biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: FPP biosynthetic process via ARBA/UniPathway mapping. Reason: Same claim as the IBA and IDA rows. Supporting Evidence: file:ARATH/FPS1/FPS1-uniprot.txt Catalyzes the sequential condensation of isopentenyl pyrophosphate with the allylic pyrophosphates, dimethylallyl pyrophosphate, and then with the resultant geranylpyrophosphate to the ultimate product farnesyl pyrophosphate. |
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Download this section (compressed HTML)Q: Does FPS1L form a distinct pool of FPP inside mitochondria that is used for ubiquinone side-chain synthesis, and in which sub-compartment (matrix or inner-membrane surface) does it act?
Q: Is the plastid HDA detection of FPS1 (PMID:28887381) a co-fractionation artefact, or is there a minor plastid-associated FPS1 pool?
Experiment: Express FPS1L-GFP from its native promoter in Arabidopsis and combine with submitochondrial fractionation (protease protection, carbonate extraction) to define where FPS1L resides and test complementation of ubiquinone levels by FPS1L versus FPS1S alone.
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