BCAT3 (BRANCHED-CHAIN AMINOTRANSFERASE 3, At3g49680) is a plastid-targeted, pyridoxal 5'-phosphate-dependent class-IV aminotransferase with a dual role in primary and specialized metabolism. As a canonical branched-chain aminotransferase it catalyzes the final, reversible transamination steps of branched-chain amino acid biosynthesis in the chloroplast, converting 4-methyl-2-oxopentanoate, (S)-3-methyl-2-oxopentanoate and 3-methyl-2-oxobutanoate to leucine, isoleucine and valine using glutamate/2-oxoglutarate; it complements the BCAA auxotrophy of a yeast bat1/bat2 mutant, and bcat3 knockouts have reduced free valine. BCAT3 also transaminates the omega-methylthio-2-oxo acids of the methionine chain-elongation cycle and is thought to catalyze the terminal transamination that converts chain-elongated 2-oxo acids to homomethionine and dihomomethionine for aliphatic glucosinolate biosynthesis; it can partly substitute for the cytosolic BCAT4 in the initial deamination of methionine, as shown by the strong additive loss of methionine-derived glucosinolates in bcat3 bcat4 double mutants. BCAT3 is expressed in the phloem, is wound-inducible and is co-expressed with BCAT4 and MAM1.
Definition: Catalysis of reversible amino-group transfer between a chain-elongated L-methionine derivative and 2-oxoglutarate, yielding the corresponding omega-methylthio-2-oxoalkanoate and L-glutamate. In methionine chain elongation, the reverse reaction produces homomethionine or longer methionine homologues from their 2-oxo acids.
Justification: GO:0010326 describes L-methionine itself and its corresponding unelongated 2-oxo acid. It does not describe the distinct elongated substrates assayed with BCAT3; the proposed term captures terminal transamination rather than backup initiation.
Parent term: transaminase activity
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | MODIFY | Summary: Root-level catalytic activity from InterPro aminotransferase signatures; true but uninformative. Reason: The catalytic claim is correct but the supported specific activities already annotated in this review are more informative descendants; refine to these activities. Proposed replacements: L-leucine:2-oxoglutarate transaminase activity L-valine:2-oxoglutarate transaminase activity L-isoleucine:2-oxoglutarate transaminase activity L-methionine:oxo-acid transaminase activity Supporting Evidence: PMID:18162591 In vitro activity tests with the recombinant protein identified highest activities with the 2-oxo acids of leucine, isoleucine, and valine, but also revealed substantial conversion of intermediates of the Met chain elongation pathway. |
| GO:0004084 branched-chain-amino-acid:2-oxoglutarate transaminase activity | IBA GO_REF:0000033 | MODIFY | Summary: PAINT inference of BCAA:2-oxoglutarate transaminase activity for the plant BCAT clade; BCAT3 is itself among the experimentally characterized descendants (its own Leu/Ile/Val transaminase EXP annotations), which is expected rather than circular. Reason: Refine this correct broad BCAA aminotransferase term to all three experimentally supported substrate-specific descendants already annotated here. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN002450258 SUPPORTS TRANSFER The ancestral claim is supported on the target; this review refines its general term using target-specific activity/localization evidence. It does not allege an erroneous IBD placement or circularity. Proposed replacements: L-leucine:2-oxoglutarate transaminase activity L-valine:2-oxoglutarate transaminase activity L-isoleucine:2-oxoglutarate transaminase activity Supporting Evidence: PMID:18162591 Highest affinities were seen toward 4MOP ( K m , 0.14 ± 0.04 m m ) and 3MOP ( K m , 0.14 ± 0.3 m m ). PMID:12068099 Restored growth on minimal medium lacking the three branched-chain amino acids confirms the respective enzymatic activities for AtBCAT-1, -2, -3, -5, and -6 |
| GO:0004084 branched-chain-amino-acid:2-oxoglutarate transaminase activity | IEA GO_REF:0000120 | MODIFY | Summary: Electronic mapping from BCAT family InterPro signatures and EC 2.6.1.42; consistent with experimental data. Reason: Refine this correct broad BCAA aminotransferase term to all three experimentally supported substrate-specific descendants already annotated here. Proposed replacements: L-leucine:2-oxoglutarate transaminase activity L-valine:2-oxoglutarate transaminase activity L-isoleucine:2-oxoglutarate transaminase activity Supporting Evidence: PMID:18162591 In vitro activity tests with the recombinant protein identified highest activities with the 2-oxo acids of leucine, isoleucine, and valine, but also revealed substantial conversion of intermediates of the Met chain elongation pathway. |
| GO:0005829 cytosol | RCA NOT PMID:21166475 Analysis of the Arabidopsis cytosolic proteome highlights su... | ACCEPT | Summary: NOT annotation (negated): BCAT3 was not found in the experimentally defined cytosolic proteome. This negative assertion agrees with the chloroplast targeting of BCAT3 shown by GFP fusion and with plastid proteomics. Reason: The absence of BCAT3 from the cytosol is consistent with its N-terminal plastid transit peptide and experimentally determined chloroplast localization; the NOT annotation is retained as correct. Supporting Evidence: PMID:21166475 defines an experimental set of plant protein sequences that are not targeted to subcellular locations following translation and folding in the cytosol PMID:12068099 In contrast, the GFP fluorescence patterns observed in protoplasts transformed with AtBCAT-2, -3, and -5:GFP constructs are congruent with the autofluorescence patterns of the chloroplasts, identifying these organelles as their subcellular residence |
| GO:0009081 branched-chain amino acid metabolic process | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping to BCAA metabolic process; BCAT3 participates in BCAA biosynthesis in plastids. Reason: Refine the broad BCAA metabolic process to the supported biosynthetic descendants already annotated; the enzyme participates catalytically rather than merely affecting amino acid abundance. Proposed replacements: L-leucine biosynthetic process L-valine biosynthetic process Supporting Evidence: PMID:18162591 In summary these data show that this enzyme does not participate exclusively in one of the two pathways. BCAT3 is clearly active in both the BCAA and the Met-derived glucosinolate biosyntheses. |
| GO:0009098 L-leucine biosynthetic process | IEA GO_REF:0000041 | ACCEPT | Summary: UniPathway mapping to L-leucine biosynthesis. BCAT3 transaminates 4-methyl-2-oxopentanoate (the Leu precursor) with the highest affinity and Vmax of all substrates tested, and complements BCAA auxotrophy in yeast. Reason: BCAT3 catalyzes the final step of Leu biosynthesis in vitro and in yeast; the authors note the in planta assignment to individual BCAAs is difficult because of redundancy with BCAT2/BCAT5, but the participation is sound. Supporting Evidence: PMID:18162591 Highest affinities were seen toward 4MOP ( K m , 0.14 ± 0.04 m m ) and 3MOP ( K m , 0.14 ± 0.3 m m ). PMID:18162591 Considering the results of the in vitro assays, the enzyme has the potential to catalyze transamination reactions forming all BCAAs. |
| GO:0009099 L-valine biosynthetic process | IEA GO_REF:0000041 | ACCEPT | Summary: UniPathway mapping to L-valine biosynthesis. bcat3-1 knockout plants have significantly reduced free Val in rosette leaves, and recombinant BCAT3 transaminates 3-methyl-2-oxobutanoate. Reason: Supported both biochemically and by the mutant phenotype (the only BCAA reduced in bcat3-1). Supporting Evidence: PMID:18162591 The reduction of Val in the bcat3-1 mutant suggests BCAT3 to be active in the formation of Val. |
| GO:0009507 chloroplast | HDA PMID:18431481 Sorting signals, N-terminal modifications and abundance of t... | MODIFY | Summary: Chloroplast proteome MS identification (Zybailov et al. 2008). Consistent with GFP targeting of BCAT3 to chloroplasts. Reason: Refine the correct general organelle assignment to chloroplast stroma, an already annotated descendant supported by stromal localization/proteomics. The original source fields are preserved. Proposed replacements: chloroplast stroma Supporting Evidence: PMID:18431481 mass spectrometry (MS) of ten independent chloroplast preparations from Arabidopsis thaliana which unambiguously identified 1325 proteins PMID:12068099 In contrast, the GFP fluorescence patterns observed in protoplasts transformed with AtBCAT-2, -3, and -5:GFP constructs are congruent with the autofluorescence patterns of the chloroplasts, identifying these organelles as their subcellular residence |
| GO:0009507 chloroplast | HDA PMID:25293756 A proteomic strategy for global analysis of plant protein co... | MODIFY | Summary: Chloroplast identification in a proteome-wide protein-complex fractionation study; consistent with established plastid localization. Reason: Refine the correct general organelle assignment to chloroplast stroma, an already annotated descendant supported by stromal localization/proteomics. The original source fields are preserved. Proposed replacements: chloroplast stroma Supporting Evidence: PMID:12068099 In contrast, the GFP fluorescence patterns observed in protoplasts transformed with AtBCAT-2, -3, and -5:GFP constructs are congruent with the autofluorescence patterns of the chloroplasts, identifying these organelles as their subcellular residence |
| GO:0009507 chloroplast | IBA GO_REF:0000033 | MODIFY | Summary: PAINT IBA for chloroplast activity of the plastid BCAT subclade (BCAT3, BCAT5); BCAT3 own localization data are among the descendant evidence. Reason: Refine the correct general organelle assignment to chloroplast stroma, an already annotated descendant supported by stromal localization/proteomics. The original source fields are preserved. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN008087559 SUPPORTS TRANSFER The ancestral claim is supported on the target; this review refines its general term using target-specific activity/localization evidence. It does not allege an erroneous IBD placement or circularity. Proposed replacements: chloroplast stroma Supporting Evidence: PMID:12068099 In contrast, the GFP fluorescence patterns observed in protoplasts transformed with AtBCAT-2, -3, and -5:GFP constructs are congruent with the autofluorescence patterns of the chloroplasts, identifying these organelles as their subcellular residence |
| GO:0009507 chloroplast | IDA PMID:12068099 The branched-chain amino acid transaminase gene family in Ar... | MODIFY | Summary: BCAT3-GFP fusion co-localizes with chloroplast autofluorescence in tobacco protoplasts (Diebold et al. 2002). Reason: Refine the correct general organelle assignment to chloroplast stroma, an already annotated descendant supported by stromal localization/proteomics. The original source fields are preserved. Proposed replacements: chloroplast stroma Supporting Evidence: PMID:12068099 In contrast, the GFP fluorescence patterns observed in protoplasts transformed with AtBCAT-2, -3, and -5:GFP constructs are congruent with the autofluorescence patterns of the chloroplasts, identifying these organelles as their subcellular residence PMID:12068099 three isoenzymes are imported into chloroplasts (AtBCAT-2, -3, and -5) |
| GO:0009507 chloroplast | IEA GO_REF:0000044 | MODIFY | Summary: UniProt subcellular location mapping (Plastid, chloroplast). Reason: Refine the correct general organelle assignment to chloroplast stroma, an already annotated descendant supported by stromal localization/proteomics. The original source fields are preserved. Proposed replacements: chloroplast stroma Supporting Evidence: PMID:12068099 In contrast, the GFP fluorescence patterns observed in protoplasts transformed with AtBCAT-2, -3, and -5:GFP constructs are congruent with the autofluorescence patterns of the chloroplasts, identifying these organelles as their subcellular residence |
| GO:0009507 chloroplast | ISM GO_REF:0000122 | MODIFY | Summary: AtSubP sequence-based prediction of chloroplast localization, consistent with the N-terminal transit peptide and experiment. Reason: Refine the correct general organelle assignment to chloroplast stroma, an already annotated descendant supported by stromal localization/proteomics. The original source fields are preserved. Proposed replacements: chloroplast stroma Supporting Evidence: PMID:12068099 In contrast, the GFP fluorescence patterns observed in protoplasts transformed with AtBCAT-2, -3, and -5:GFP constructs are congruent with the autofluorescence patterns of the chloroplasts, identifying these organelles as their subcellular residence |
| GO:0009570 chloroplast stroma | HDA PMID:20061580 AT_CHLORO, a comprehensive chloroplast proteome database wit... | ACCEPT | Summary: Identified in the stromal subfraction of purified chloroplasts (AT_CHLORO). A soluble aminotransferase acting on stromal BCAA and methionine-elongation intermediates is expected in the stroma. Reason: HDA sub-plastid localization consistent with a soluble plastid enzyme. Supporting Evidence: PMID:20061580 We went a step further into the knowledge of the chloroplast proteome by focusing, in the same set of experiments, on the localization of proteins in the stroma, the thylakoids, and envelope membranes. |
| GO:0010326 L-methionine:oxo-acid transaminase activity | EXP PMID:18162591 Arabidopsis branched-chain aminotransferase 3 functions in b... | ACCEPT | Summary: Recombinant BCAT3 transaminates 4-methylthio-2-oxobutanoate (MTOB), the 2-oxo acid of methionine (Km 1.92 mM), and genetic data indicate BCAT3 can partially take over the Met-to-MTOB step from BCAT4. Reason: Experimentally supported secondary activity of BCAT3; it underlies its backup role in the first step of methionine chain elongation. BCAT3 also acts on longer omega-methylthio-2-oxo acids, for which GO has no more specific term. Supporting Evidence: PMID:18162591 These values are in the range of those found for MTOB ( K m , 1.92 ± 0.27 m m PMID:18162591 This strongly suggests that BCAT3 can act as a backup of BCAT4 by transaminating Met to MTOB and thus contributes to the overall biosynthesis of Met-derived aliphatic glucosinolates, which is probably localized in plastids. |
| GO:0010326 L-methionine:oxo-acid transaminase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic mapping from EC 2.6.1.88 / RHEA:31763 in the UniProt entry, based on the experimental data for BCAT3. Reason: Consistent with experimental MTOB transamination. Supporting Evidence: PMID:18162591 In vitro activity tests with the recombinant protein identified highest activities with the 2-oxo acids of leucine, isoleucine, and valine, but also revealed substantial conversion of intermediates of the Met chain elongation pathway. |
| GO:0052654 L-leucine:2-oxoglutarate transaminase activity | EXP PMID:18162591 Arabidopsis branched-chain aminotransferase 3 functions in b... | ACCEPT | Summary: Recombinant BCAT3 transaminates 4-methyl-2-oxopentanoate/leucine with the highest affinity and rate of any substrate tested. Reason: Direct enzyme assay; specific child of the core BCAA transaminase activity. Supporting Evidence: PMID:18162591 Highest affinities were seen toward 4MOP ( K m , 0.14 ± 0.04 m m ) and 3MOP ( K m , 0.14 ± 0.3 m m ). |
| GO:0052654 L-leucine:2-oxoglutarate transaminase activity | IEA GO_REF:0000116 | ACCEPT | Summary: Rhea-based electronic mapping (RHEA:18321), consistent with experiment. Reason: Consistent with direct assay. Supporting Evidence: PMID:18162591 Highest affinities were seen toward 4MOP ( K m , 0.14 ± 0.04 m m ) and 3MOP ( K m , 0.14 ± 0.3 m m ). |
| GO:0052655 L-valine:2-oxoglutarate transaminase activity | EXP PMID:18162591 Arabidopsis branched-chain aminotransferase 3 functions in b... | ACCEPT | Summary: Recombinant BCAT3 transaminates 3-methyl-2-oxobutanoate (Val precursor), with lower affinity (Km 1.38 mM) than for the Leu/Ile keto acids; bcat3 plants have reduced Val. Reason: Direct enzyme assay plus consistent mutant phenotype. Supporting Evidence: PMID:18162591 A substantially lower affinity and maximal velocity was measured for 3MOB, the keto acid of Val PMID:18162591 The reduction of Val in the bcat3-1 mutant suggests BCAT3 to be active in the formation of Val. |
| GO:0052655 L-valine:2-oxoglutarate transaminase activity | IEA GO_REF:0000116 | ACCEPT | Summary: Rhea-based electronic mapping (RHEA:24813), consistent with experiment. Reason: Consistent with direct assay. Supporting Evidence: PMID:18162591 The reduction of Val in the bcat3-1 mutant suggests BCAT3 to be active in the formation of Val. |
| GO:0052656 L-isoleucine:2-oxoglutarate transaminase activity | EXP PMID:18162591 Arabidopsis branched-chain aminotransferase 3 functions in b... | ACCEPT | Summary: Recombinant BCAT3 transaminates (S)-3-methyl-2-oxopentanoate (Ile precursor) with high affinity (Km 0.14 mM). Reason: Direct enzyme assay. Supporting Evidence: PMID:18162591 Highest affinities were seen toward 4MOP ( K m , 0.14 ± 0.04 m m ) and 3MOP ( K m , 0.14 ± 0.3 m m ). |
| GO:0052656 L-isoleucine:2-oxoglutarate transaminase activity | IEA GO_REF:0000116 | ACCEPT | Summary: Rhea-based electronic mapping (RHEA:24801), consistent with experiment. Reason: Consistent with direct assay. Supporting Evidence: PMID:18162591 Highest affinities were seen toward 4MOP ( K m , 0.14 ± 0.04 m m ) and 3MOP ( K m , 0.14 ± 0.3 m m ). |
| GO:0019761 glucosinolate biosynthetic process | IMP PMID:18162591 Arabidopsis branched-chain aminotransferase 3 functions in b... | NEW | Summary: BCAT3 has no glucosinolate-biosynthesis annotation in GOA, although Knill et al. (2008) show it transaminates methionine chain-elongation intermediates, that bcat3-1 alters the aliphatic glucosinolate chain-length profile, and that bcat3 bcat4 double mutants lose substantially more methionine-derived glucosinolate than bcat4 alone. Reason: BCAT3 itself performs transamination, established by recombinant activity plus metabolite genetics (PMID:18162591), rather than being consumed or merely required. Live QuickGO comparator audit: equivalent methionine-chain transaminase BCAT4 has GO:0019761 (PMID:17056707), while BCAT6 lacks it; this mixed pattern is not a systematic substrate-exclusion convention and absence alone is not evidence of a gap. The term is under biosynthesis/sulfur-compound metabolism, fitting this catalytic role. No Q9M401 activity occurs in gocams/index.tsv. No existing or proposed ancestor/descendant BP duplicates this proposal. Direct target activity, not pathway completeness, justifies retaining this pre-existing NEW row. Supporting Evidence: PMID:18162591 In summary these data show that this enzyme does not participate exclusively in one of the two pathways. BCAT3 is clearly active in both the BCAA and the Met-derived glucosinolate biosyntheses. PMID:18162591 Third, in the bcat3-1/bcat4-2 double mutant ( Tables IX and X ), the knockout of BCAT3 has a striking additive effect on the reduction of total Met-derived glucosinolate content in comparison to the bcat4-1 or bcat4-2 single knockout mutants. |
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Download this section (compressed HTML)Q: Which transamination steps of the methionine chain-elongation cycle does BCAT3 catalyze in planta versus BCAT4, and which amino donor (Glu or a BCAA) is used in the plastid?
Q: How is BCAT3 partitioned between BCAA biosynthesis and glucosinolate chain elongation, and do Ser/Thr-derived imines that inhibit BCAT3 regulate this balance?
Q: GO has an unused term, GO:0033322 L-homomethionine biosynthetic process, whose definition (formation of L-homomethionine from L-methionine by chain elongation) matches the methionine chain-elongation cycle this enzyme catalyzes. GO obsoleted the related terms GO:0033506 (glucosinolate biosynthetic process from homomethionine; a pathway variant out of scope, replaced by GO:0019761) and GO:0033321 (homomethionine metabolic process; unnecessary grouping), and no gene product in any species carries GO:0033322. Should the chain-elongation enzymes (BCAT4, MAM1/MAM3, IPMI, IPMDH1, BCAT3) be annotated to it, or should GO obsolete it in favour of glucosinolate biosynthetic process?
Experiment: Assay recombinant BCAT3 with the complete series of chain-elongated omega-methylthio-2-oxo acids (C5-C9) in the reverse (amination) direction with glutamate to test the proposed terminal transamination role.
Experiment: Profile chain-elongated methionine homologs (homo-, dihomo-, trihomomethionine) in bcat3, bcat4 and bcat3 bcat4 plants to directly measure the products of the elongation cycle rather than downstream glucosinolates.
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