ACO2 encodes a mitochondrial paralog of aconitase (aconitase/IPM isomerase family, [4Fe-4S]) that has specialised as a homocitrate dehydratase in the alpha-aminoadipate pathway of lysine biosynthesis. Purified Aco2p reversibly converts (R)-homocitrate to cis-homoaconitate, which homoaconitase (Lys4p) then hydrates to homoisocitrate; it is about 950-fold more active with homoaconitate than with cis-aconitate, a specificity attributed to an active-site lysine (K610) in place of the arginine of TCA-cycle aconitases. Aco2p cannot replace Aco1p in the TCA cycle (it does not rescue the glutamate auxotrophy of aco1 mutants). ACO2 is expressed mainly during glucose growth, and aco2 deletion causes a fitness defect under glucose-limited (trehalose) respiro-fermentative growth with modest changes in aconitate and 2-oxoglutarate, which has been interpreted as a minor aconitase contribution.
Definition: Catalysis of the reaction: (2R)-homocitrate = cis-homoaconitate + H2O.
Justification: GO:0004409 homoaconitate hydratase activity is defined as the homoisocitrate <-> cis-homoaconitate reaction (EC 4.2.1.36, Lys4p). The preceding dehydration of (R)-homocitrate (RHEA:26101) has no GO term, yet it is the physiological activity of yeast Aco2p and is also performed by fungal and Thermus aconitases.
Parent term: hydro-lyase activity
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003994 aconitate hydratase activity | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: PAINT IBA from the aconitase node PTN000186533, which covers both yeast paralogs. Aco2p retains low aconitase activity in vitro (~950-fold lower than with homoaconitate), so the inherited activity is not wrong, but it is not the physiological function of this paralog, which specialised on homocitrate. Reason: Weak residual activity; physiological activity is homocitrate dehydratase (no GO term yet). Supporting Evidence: PMID:23106124 Interestingly, Aco2p was highly active with homoaconitate and displayed a 950-fold higher specific activity with homoaconitate than with aconitate. PMID:23106124 This is also in agreement with the high in vitro activity of Aco2p with homoaconitate compared to its low activity with aconitate (Table 1). |
| GO:0003994 aconitate hydratase activity | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO (IPR006248 mitochondrial-like aconitase) mapping. Domain-based transfer cannot distinguish the homocitrate-specialised Aco2 subfamily; Aco2p has only low aconitase activity. Reason: Residual activity only; family-level transfer. Supporting Evidence: PMID:23106124 Interestingly, Aco2p was highly active with homoaconitate and displayed a 950-fold higher specific activity with homoaconitate than with aconitate. |
| GO:0003994 aconitate hydratase activity | ISS PMID:14576278 The proteome of Saccharomyces cerevisiae mitochondria. | KEEP AS NON CORE | Summary: ISS assigned by the mitochondrial proteome paper (Sickmann et al. 2003) by similarity to aconitase. Biochemistry later showed Aco2p strongly prefers homoaconitate over aconitate. Reason: Sequence-similarity call superseded by direct biochemistry; residual activity only. Supporting Evidence: PMID:23106124 Interestingly, Aco2p was highly active with homoaconitate and displayed a 950-fold higher specific activity with homoaconitate than with aconitate. |
| GO:0003994 aconitate hydratase activity | RCA GO_REF:0000123 | MARK AS OVER ANNOTATED | Summary: YeastPathways RCA placing Aco2p in the glyoxylate cycle. No evidence links Aco2p to the glyoxylate shunt; the cytosolic shunt aconitase is Aco1p, and Aco2p is mitochondrial and homocitrate-specialised. Reason: YeastCyc attaches the paralog to the reaction without yeast evidence. Supporting Evidence: PMID:23106124 Aco2p specifically and exclusively contributes to lysine biosynthesis PMID:15975908 Together, our data indicate that yeast aconitase isoenzymes distribute between two distinct subcellular compartments and participate in two separate metabolic pathways; the glyoxylate shunt in the cytosol and the TCA cycle in mitochondria. |
| GO:0003994 aconitate hydratase activity | RCA GO_REF:0000123 | KEEP AS NON CORE | Summary: YeastPathways RCA from the TCA/glyoxylate superpathway (PWY3O-94). Aco2p has measurable but low aconitase activity; the pathway attribution is superpathway-inherited. Reason: Residual activity; pathway role marginal. Supporting Evidence: PMID:23106124 This is also in agreement with the high in vitro activity of Aco2p with homoaconitate compared to its low activity with aconitate (Table 1). |
| GO:0003994 aconitate hydratase activity | RCA GO_REF:0000123 | KEEP AS NON CORE | Summary: YeastPathways RCA from the TCA cycle (TCA-EUK-PWY). Fazius et al. conclude Aco2p does not contribute to the citric acid cycle, whereas Chen et al. report a modest aconitase-like metabolic phenotype under glucose limitation; the activity class is retained only as a minor function. Reason: Disputed minor contribution; not core. Supporting Evidence: PMID:23106124 As Aco2p does not contribute to the citric acid cycle, it cannot recover glutamate auxotrophy derived from aco1 deletion. PMID:30834327 Consistent with lowered aconitase activity, the aconitate levels were somewhat elevated and Ξ±-ketoglutarate depleted (Fig. 4C). |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | REMOVE | Summary: Large-scale interactome study (Michaelis et al. 2023) reporting a binary interaction; UniProt lists an interaction with the Fe-S carrier NFU1, plausibly reflecting cluster delivery. 'protein binding' conveys no functional information. Reason: Uninformative term per curation policy; removal does not imply the interaction is false. Supporting Evidence: file:yeast/ACO2/ACO2-uniprot.txt P39533; P32860: NFU1; NbExp=2; |
| GO:0005739 mitochondrion | HDA PMID:14562095 Global analysis of protein localization in budding yeast. | ACCEPT | Summary: Genome-wide GFP localisation (Huh et al. 2003) placed Aco2p in mitochondria. Reason: Correct location. Supporting Evidence: file:yeast/ACO2/ACO2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14562095, |
| GO:0005739 mitochondrion | HDA PMID:14576278 The proteome of Saccharomyces cerevisiae mitochondria. | ACCEPT | Summary: Mitochondrial proteome (Sickmann et al. 2003) detected Aco2p in purified mitochondria. Reason: Correct location. Supporting Evidence: file:yeast/ACO2/ACO2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14562095, |
| GO:0005739 mitochondrion | HDA PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimen... | ACCEPT | Summary: Mitochondrial proteome (Reinders et al. 2006) detected Aco2p. Reason: Correct location. Supporting Evidence: file:yeast/ACO2/ACO2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14562095, |
| GO:0005739 mitochondrion | HDA PMID:24769239 Quantitative variations of the mitochondrial proteome and ph... | ACCEPT | Summary: Quantitative mitochondrial proteome (Renvoise et al. 2014) detected Aco2p. Reason: Correct location. Supporting Evidence: file:yeast/ACO2/ACO2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14562095, |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA is_active_in mitochondrion; correct for this mitochondrial homocitrate dehydratase. Reason: Correct location. Supporting Evidence: file:yeast/ACO2/ACO2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14562095, |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping to mitochondrion; correct. Reason: Correct location. Supporting Evidence: file:yeast/ACO2/ACO2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14562095, |
| GO:0005829 cytosol | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: PAINT IBA is_active_in cytosol (PTN001705783). The cytosolic pool documented for yeast aconitase concerns Aco1p; there is no evidence for cytosolic Aco2p, which carries a mitochondrial presequence and is found in mitochondrial proteomes. Reason: No target-specific support for a cytosolic pool. Propagation Review Root cause: PROPAGATION BAD Failure modes: WRONG ORTHOLOG OR PARALOG COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN001705783 SUPPORTS SOURCE BUT NOT TARGET Cytosolic aconitase pool documented in yeast is Aco1p; Aco2p is a mitochondrial paralog with no cytosolic evidence. Supporting Evidence: file:yeast/ACO2/ACO2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14562095, |
| GO:0005829 cytosol | RCA GO_REF:0000123 | REMOVE | Summary: YeastPathways RCA cytosol from the glyoxylate cycle; Aco2p has no glyoxylate-cycle role and no cytosolic localisation evidence. Reason: Superpathway/paralog artefact contradicted by mitochondrial localisation. Supporting Evidence: file:yeast/ACO2/ACO2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14562095, PMID:23106124 Aco2p specifically and exclusively contributes to lysine biosynthesis |
| GO:0005829 cytosol | RCA GO_REF:0000123 | REMOVE | Summary: YeastPathways RCA cytosol from the TCA/glyoxylate superpathway; not supported for Aco2p, which is mitochondrial. Reason: Superpathway artefact. Supporting Evidence: file:yeast/ACO2/ACO2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14562095, |
| GO:0005829 cytosol | RCA GO_REF:0000123 | REMOVE | Summary: YeastPathways RCA cytosol from the TCA cycle pathway; the TCA cycle is mitochondrial and Aco2p is mitochondrial. Reason: Wrong compartment. Supporting Evidence: file:yeast/ACO2/ACO2-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14562095, |
| GO:0006097 glyoxylate cycle | RCA GO_REF:0000123 | MARK AS OVER ANNOTATED | Summary: YeastPathways RCA involved_in glyoxylate cycle; no evidence Aco2p participates (the shunt aconitase is cytosolic Aco1p). Reason: Paralog attached to pathway without yeast evidence. Supporting Evidence: PMID:23106124 Aco2p specifically and exclusively contributes to lysine biosynthesis PMID:15975908 Together, our data indicate that yeast aconitase isoenzymes distribute between two distinct subcellular compartments and participate in two separate metabolic pathways; the glyoxylate shunt in the cytosol and the TCA cycle in mitochondria. |
| GO:0006099 tricarboxylic acid cycle | IEA GO_REF:0000120 | MARK AS OVER ANNOTATED | Summary: Combined IEA (ARBA, InterPro IPR006248) for TCA cycle. Family-based transfer that does not separate the homocitrate-specialised Aco2 subfamily; Fazius et al. show Aco2p cannot sustain the TCA cycle in aco1 mutants. Reason: Over-propagated from TCA aconitases; contradicted for this paralog. Supporting Evidence: PMID:23106124 As Aco2p does not contribute to the citric acid cycle, it cannot recover glutamate auxotrophy derived from aco1 deletion. PMID:23106124 Thus, the conversion of arginine to lysine diminishes citric acid cycle aconitase activity and explains why the Aco2p protein cannot restore glutamate prototrophy of aco1 mutants. |
| GO:0006099 tricarboxylic acid cycle | IMP PMID:30834327 Minor Isozymes Tailor Yeast Metabolism to Carbon Availabilit... | KEEP AS NON CORE | Summary: Chen et al. (2019) reported that aco2 deletion causes a 25% fitness defect on trehalose (glucose-limited, respiro-fermentative growth) with slightly raised aconitate and lowered 2-oxoglutarate, and interpreted ACO2 as a minor aconitase. Fazius et al. found Aco2p does not contribute to the citric acid cycle. Defer to the curator but treat as a minor, condition-specific contribution. Reason: Experimental annotation retained; contribution is disputed and not the specialised core role. Supporting Evidence: PMID:30834327 On trehalose, the aco2Ξ deletion had a fitness disadvantage of 25% (Fig. 4B), confirming that this aconitase isozyme supports glycolytic respiration. PMID:30834327 Consistent with lowered aconitase activity, the aconitate levels were somewhat elevated and Ξ±-ketoglutarate depleted (Fig. 4C). PMID:23106124 As Aco2p does not contribute to the citric acid cycle, it cannot recover glutamate auxotrophy derived from aco1 deletion. |
| GO:0009060 aerobic respiration | RCA GO_REF:0000123 | MARK AS OVER ANNOTATED | Summary: YeastPathways RCA involved_in aerobic respiration from TCA-EUK-PWY; superpathway inheritance to a paralog whose main role is lysine biosynthesis. Reason: Over-general and weakly supported for Aco2p. Supporting Evidence: PMID:23106124 Aco2p specifically and exclusively contributes to lysine biosynthesis |
| GO:0051539 4 iron, 4 sulfur cluster binding | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA from the aconitase node PTN000186533, which covers both yeast paralogs for [4Fe-4S] cluster binding; the cluster ligands are conserved in Aco2p, which is enzymatically active. Reason: Correct cofactor binding. Supporting Evidence: file:yeast/ACO2/ACO2-uniprot.txt Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883; |
| GO:0051539 4 iron, 4 sulfur cluster binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO (IPR006248) mapping to 4Fe-4S cluster binding; correct for this active aconitase-family enzyme. Reason: Correct cofactor binding. Supporting Evidence: file:yeast/ACO2/ACO2-uniprot.txt Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883; |
| GO:0009085 L-lysine biosynthetic process | IDA PMID:23106124 The fungal Ξ±-aminoadipate pathway for lysine biosynthesis re... | NEW | Summary: Fazius et al. showed purified Aco2p converts homocitrate to homoaconitate (assayed as homoaconitate hydration coupled to Lys4p) and that aco2 mutants depend more strongly on lysine than aco1 mutants; Aco2p itself catalyses a step of the alpha-aminoadipate pathway, so this is participation, not mere requirement. GOA carries no lysine-biosynthesis process for ACO2. Reason: Aco2p performs the homocitrate dehydration step of lysine biosynthesis. Supporting Evidence: PMID:23106124 Aco2p specifically and exclusively contributes to lysine biosynthesis PMID:23106124 Interestingly, Aco2p was highly active with homoaconitate and displayed a 950-fold higher specific activity with homoaconitate than with aconitate. |
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Download this section (compressed HTML)Q: Does the aco2 fitness defect on limiting glucose reflect a genuine aconitase (TCA) contribution or an indirect effect of reduced lysine/2-oxoglutarate balance via the homocitrate step?
Experiment: Measure lysine requirement and TCA flux (13C-glucose) in aco2 and aco2-K610R strains on trehalose to separate homocitrate-dehydratase from aconitase contributions.
Hypothesis: The physiological contribution of Aco2p is via homocitrate dehydration rather than citrate isomerisation.
Putative mitochondrial aconitase isozyme; similarity to Aco1p, an aconitase required for the TCA cycle; expression induced during growth on glucose, by amino acid starvation via Gcn4p, and repressed on ethanol
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