CIT2 encodes the peroxisomal (extramitochondrial) citrate synthase of Saccharomyces cerevisiae. Cit2p condenses acetyl-CoA, including acetyl-CoA generated by peroxisomal beta-oxidation, with oxaloacetate to form citrate for the glyoxylate cycle, and is required for efficient lipid mobilisation on oleate. It carries a C-terminal SKL peroxisomal targeting signal and a cryptic N-terminal signal, and is also found in the cytosol. CIT2 is induced by C2 carbon sources; in glucose-grown cells Cit2p is degraded via the SCF(Ucc1) ubiquitin ligase, a regulation relieved by oxaloacetate. Cit2p can substitute for the mitochondrial isozyme Cit1p in supplying citrate for glutamate synthesis, so only cit1 cit2 double mutants are glutamate auxotrophs. It may also have weak methylcitrate synthase activity. CIT2 is the founding target of the mitochondria-to-nucleus retrograde (RTG) response; its expression rises when mitochondrial function is reduced, through an upstream UASr element and the Rtg1 and Rtg2 proteins.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005737 cytoplasm | IDA PMID:25982115 The Ubiquitin Ligase SCF(Ucc1) Acts as a Metabolic Switch fo... | ACCEPT | Summary: Nakatsukasa et al. observed Cit2p in the cytoplasm as well as peroxisomes, the cytosolic pool being the target of SCF(Ucc1)-mediated degradation in glucose-grown cells. Reason: Experimental location. Supporting Evidence: file:yeast/CIT2/CIT2-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:25982115}. PMID:25982115 mediates proteasomal degradation of citrate synthase in the glyoxylate cycle to maintain metabolic homeostasis in glucose-grown cells |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping to cytoplasm; consistent with experimental data. Reason: Correct. Supporting Evidence: file:yeast/CIT2/CIT2-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:25982115}. |
| GO:0005739 mitochondrion | HDA PMID:14576278 The proteome of Saccharomyces cerevisiae mitochondria. | KEEP AS NON CORE | Summary: Mitochondrial proteome (Sickmann et al. 2003) detected Cit2p in mitochondrial preparations. Cit2p has a cryptic N-terminal mitochondrial targeting capacity, but its physiological location is peroxisomal/cytosolic; detection may reflect contamination or a minor pool. Reason: High-throughput detection; not the main location. Supporting Evidence: PMID:16877773 contains a cryptic targeting signal for both peroxisomes (PTS) and mitochondria (MTS) within its 20-amino acid N-terminal segment |
| GO:0005739 mitochondrion | HDA PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimen... | KEEP AS NON CORE | Summary: Mitochondrial proteome (Reinders et al. 2006) detected Cit2p; same caveat as other proteomic mitochondrial calls. Reason: Minor/uncertain pool. Supporting Evidence: PMID:16877773 contains a cryptic targeting signal for both peroxisomes (PTS) and mitochondria (MTS) within its 20-amino acid N-terminal segment |
| GO:0005739 mitochondrion | RCA GO_REF:0000123 | MARK AS OVER ANNOTATED | Summary: YeastPathways RCA is_active_in mitochondrion from the TCA cycle pathway, assigning Cit2p to mitochondrial TCA-cycle activity. Cit2p is the peroxisomal isozyme; mitochondrial citrate synthase activity is Cit1p (and Cit3p). Reason: Paralog attached to mitochondrial pathway context. Supporting Evidence: PMID:2181273 We conclude that citrate synthase encoded by CIT2 is peroxisomal and participates in the glyoxylate cycle. PMID:2181273 The peroxisomal activity, but not the mitochondrial activity, was inhibited by incubation at pH 8.1, a characteristic of the extramitochondrial citrate synthase encoded by the CIT2 gene. |
| GO:0005759 mitochondrial matrix | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: PAINT IBA is_active_in mitochondrial matrix from the citrate synthase node. Cit2p diverged to a peroxisomal role (SKL signal); target-specific evidence places its activity in peroxisomes. Reason: Inherited location contradicted by target-specific localisation. Propagation Review Root cause: PROPAGATION BAD Failure modes: COMPARTMENT OR COMPLEX MISMATCH FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN000201222 SUPPORTS SOURCE BUT NOT TARGET Matrix location holds for Cit1p/Cit3p; Cit2p carries a PTS1 (SKL) and acts in peroxisomes. Supporting Evidence: PMID:2181273 We conclude that citrate synthase encoded by CIT2 is peroxisomal and participates in the glyoxylate cycle. |
| GO:0005777 peroxisome | EXP PMID:2181273 Citrate synthase encoded by the CIT2 gene of Saccharomyces c... | ACCEPT | Summary: Lewin et al. showed Cit2p citrate synthase activity co-sediments with peroxisomes from oleate-grown cells (EXP). Reason: Experimental location. Supporting Evidence: PMID:2181273 We conclude that citrate synthase encoded by CIT2 is peroxisomal and participates in the glyoxylate cycle. PMID:2181273 The peroxisomal activity, but not the mitochondrial activity, was inhibited by incubation at pH 8.1, a characteristic of the extramitochondrial citrate synthase encoded by the CIT2 gene. |
| GO:0005777 peroxisome | IDA PMID:16877773 Mutational and functional analysis of the cryptic N-terminal... | ACCEPT | Summary: Lee et al. used GFP fusions showing the Cit2p N-terminal segment and SKL direct peroxisomal targeting. Reason: Experimental location. Supporting Evidence: PMID:16877773 contains a cryptic targeting signal for both peroxisomes (PTS) and mitochondria (MTS) within its 20-amino acid N-terminal segment |
| GO:0005777 peroxisome | IDA PMID:25982115 The Ubiquitin Ligase SCF(Ucc1) Acts as a Metabolic Switch fo... | ACCEPT | Summary: Nakatsukasa et al. observed peroxisomal Cit2p. Reason: Experimental location. Supporting Evidence: PMID:25982115 mediates proteasomal degradation of citrate synthase in the glyoxylate cycle to maintain metabolic homeostasis in glucose-grown cells |
| GO:0005777 peroxisome | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular location mapping to peroxisome; correct. Reason: Correct. Supporting Evidence: PMID:2181273 We conclude that citrate synthase encoded by CIT2 is peroxisomal and participates in the glyoxylate cycle. |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA cytosol from the glyoxylate cycle; Cit2p has a cytosolic pool and glyoxylate-cycle enzymes in yeast are distributed between cytosol and peroxisomes. Reason: Consistent with experimental data. Supporting Evidence: file:yeast/CIT2/CIT2-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:25982115}. |
| GO:0005829 cytosol | RCA GO_REF:0000123 | KEEP AS NON CORE | Summary: YeastPathways RCA cytosol from the TCA/glyoxylate superpathway (PWY3O-94); redundant with direct evidence. Reason: Superpathway-inherited; redundant. Supporting Evidence: file:yeast/CIT2/CIT2-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:25982115}. |
| GO:0005975 carbohydrate metabolic process | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: PAINT IBA carbohydrate metabolic process on the citrate synthase node; vague grouping that adds nothing beyond glyoxylate cycle. Reason: Uninformative over-general process. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000201223 SUPPORTS TRANSFER Node-level grouping term; vague rather than wrong. Supporting Evidence: PMID:2181273 We conclude that citrate synthase encoded by CIT2 is peroxisomal and participates in the glyoxylate cycle. |
| GO:0006097 glyoxylate cycle | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA glyoxylate cycle; directly supported by Lewin et al., who concluded Cit2p participates in the glyoxylate cycle. Reason: Core process. Supporting Evidence: PMID:2181273 We conclude that citrate synthase encoded by CIT2 is peroxisomal and participates in the glyoxylate cycle. |
| GO:0006099 tricarboxylic acid cycle | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: PAINT IBA tricarboxylic acid cycle. Cit2p is not a mitochondrial TCA-cycle enzyme; it can supply citrate for glutamate synthesis when Cit1p is absent, but its physiological pathway is the glyoxylate cycle. Reason: Family-level process not representative of this peroxisomal paralog. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN000201223 SUPPORTS SOURCE BUT NOT TARGET TCA-cycle role holds for mitochondrial citrate synthases; the peroxisomal Cit2p paralog serves the glyoxylate cycle. Supporting Evidence: PMID:2181273 We conclude that citrate synthase encoded by CIT2 is peroxisomal and participates in the glyoxylate cycle. PMID:3023912 Therefore, the citrate synthase produced from either gene was sufficient for these metabolic roles. |
| GO:0006099 tricarboxylic acid cycle | IEA GO_REF:0000120 | MARK AS OVER ANNOTATED | Summary: Combined IEA (InterPro IPR010109, UniPathway UPA00223) TCA cycle; same issue as the IBA. Reason: Not representative of the peroxisomal paralog. Supporting Evidence: PMID:2181273 We conclude that citrate synthase encoded by CIT2 is peroxisomal and participates in the glyoxylate cycle. |
| GO:0006101 citrate metabolic process | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: Combined IEA citrate metabolic process; correct (Cit2p makes citrate) but general. Reason: Correct but general. Supporting Evidence: file:yeast/CIT2/CIT2-uniprot.txt Reaction=oxaloacetate + acetyl-CoA + H2O = citrate + CoA + H(+); |
| GO:0006101 citrate metabolic process | IGI PMID:12913175 Modulation of citrate metabolism alters aluminum tolerance i... | KEEP AS NON CORE | Summary: Anoop et al.: citrate synthase triple mutant (cit1 cit2 cit3) accumulates less citrate; supports a role in citrate production. Reason: Correct but general. Supporting Evidence: PMID:12913175 A triple mutant of CS (Deltacit123) showed lower levels of citrate accumulation and reduced Al tolerance |
| GO:0006101 citrate metabolic process | IGI PMID:12913175 Modulation of citrate metabolism alters aluminum tolerance i... | KEEP AS NON CORE | Summary: Second IGI row from PMID:12913175 (different interacting gene). Reason: Correct but general. Supporting Evidence: PMID:12913175 A triple mutant of CS (Deltacit123) showed lower levels of citrate accumulation and reduced Al tolerance |
| GO:0009060 aerobic respiration | RCA GO_REF:0000123 | MARK AS OVER ANNOTATED | Summary: YeastPathways RCA aerobic respiration from TCA-EUK-PWY; Cit2p is not part of the mitochondrial TCA cycle/respiration. Reason: Paralog attached to mitochondrial pathway. Supporting Evidence: PMID:2181273 We conclude that citrate synthase encoded by CIT2 is peroxisomal and participates in the glyoxylate cycle. |
| GO:0036440 citrate synthase activity | EXP PMID:3023912 Saccharomyces cerevisiae contains two functional citrate syn... | ACCEPT | Summary: Kim et al. isolated CIT2 as a second functional citrate synthase gene; either CIT1 or CIT2 suffices for glutamate prototrophy. Reason: Experimental evidence. Supporting Evidence: PMID:3023912 Disruption of both genes in the yeast genome was necessary to produce classical citrate synthase-deficient phenotypes: glutamate auxotrophy and poor growth on rich medium containing lactate, a nonfermentable carbon source. PMID:3023912 Therefore, the citrate synthase produced from either gene was sufficient for these metabolic roles. |
| GO:0036440 citrate synthase activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA citrate synthase activity; Cit2p is an active citrate synthase. Reason: Core activity. Supporting Evidence: file:yeast/CIT2/CIT2-uniprot.txt Reaction=oxaloacetate + acetyl-CoA + H2O = citrate + CoA + H(+); PMID:2181273 The peroxisomal activity, but not the mitochondrial activity, was inhibited by incubation at pH 8.1, a characteristic of the extramitochondrial citrate synthase encoded by the CIT2 gene. |
| GO:0036440 citrate synthase activity | IDA PMID:2181273 Citrate synthase encoded by the CIT2 gene of Saccharomyces c... | ACCEPT | Summary: Lewin et al. measured pH 8.1-sensitive citrate synthase activity specific to the CIT2 product in peroxisomal fractions. Reason: Direct assay. Supporting Evidence: PMID:2181273 The peroxisomal activity, but not the mitochondrial activity, was inhibited by incubation at pH 8.1, a characteristic of the extramitochondrial citrate synthase encoded by the CIT2 gene. |
| GO:0036440 citrate synthase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Combined IEA (Rhea:16845, EC 2.3.3.16); correct. Reason: Core activity. Supporting Evidence: file:yeast/CIT2/CIT2-uniprot.txt Reaction=oxaloacetate + acetyl-CoA + H2O = citrate + CoA + H(+); |
| GO:0036440 citrate synthase activity | IGI PMID:2181273 Citrate synthase encoded by the CIT2 gene of Saccharomyces c... | ACCEPT | Summary: Lewin et al.: in a cit1 disruption strain all remaining activity was the pH 8.1-sensitive (Cit2p) activity in peroxisomes. Reason: Genetic evidence. Supporting Evidence: PMID:2181273 The peroxisomal activity, but not the mitochondrial activity, was inhibited by incubation at pH 8.1, a characteristic of the extramitochondrial citrate synthase encoded by the CIT2 gene. |
| GO:0036440 citrate synthase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA glyoxylate cycle (GLYOXYLATE-BYPASS); correct activity in the correct pathway. Reason: Correct. Supporting Evidence: PMID:2181273 We conclude that citrate synthase encoded by CIT2 is peroxisomal and participates in the glyoxylate cycle. |
| GO:0036440 citrate synthase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA TCA/glyoxylate superpathway; activity class correct. Reason: Correct activity class. Supporting Evidence: file:yeast/CIT2/CIT2-uniprot.txt Reaction=oxaloacetate + acetyl-CoA + H2O = citrate + CoA + H(+); |
| GO:0036440 citrate synthase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA TCA cycle pathway; activity class correct (pathway/compartment caveats handled on BP/CC rows). Reason: Correct activity class. Supporting Evidence: file:yeast/CIT2/CIT2-uniprot.txt Reaction=oxaloacetate + acetyl-CoA + H2O = citrate + CoA + H(+); |
| GO:0042802 identical protein binding | IPI PMID:10688190 A comprehensive analysis of protein-protein interactions in ... | KEEP AS NON CORE | Summary: Uetz et al. large-scale two-hybrid self-interaction. Citrate synthases are obligate homodimers, so self-association is expected. Reason: Consistent with dimeric enzyme; non-core. Supporting Evidence: PMID:28076776 We find that phosphorylation of S462 can eliminate Cit1p enzymatic activity likely by disrupting its proper dimerization, and that Ptc7p-driven dephosphorylation rescues Cit1p activity. |
| GO:0042802 identical protein binding | IPI PMID:18467557 An in vivo map of the yeast protein interactome. | KEEP AS NON CORE | Summary: Tarassov et al. in vivo PCA self-interaction of Cit2p; consistent with homodimeric citrate synthase. Reason: Consistent with dimeric enzyme; non-core. Supporting Evidence: PMID:28076776 We find that phosphorylation of S462 can eliminate Cit1p enzymatic activity likely by disrupting its proper dimerization, and that Ptc7p-driven dephosphorylation rescues Cit1p activity. |
| GO:0042802 identical protein binding | IPI PMID:31454312 The role of structural pleiotropy and regulatory evolution i... | KEEP AS NON CORE | Summary: Self-interaction from a paralog/structural-pleiotropy study (Marchant et al. 2019); consistent with dimeric citrate synthase. Reason: Consistent with dimeric enzyme; non-core. Supporting Evidence: PMID:28076776 We find that phosphorylation of S462 can eliminate Cit1p enzymatic activity likely by disrupting its proper dimerization, and that Ptc7p-driven dephosphorylation rescues Cit1p activity. |
| GO:0046912 acyltransferase activity, acyl groups converted into alkyl on transfer | IEA GO_REF:0000120 | MODIFY | Summary: Combined IEA for the EC 2.3.3 parent 'acyltransferase activity, acyl groups converted into alkyl on transfer'; correct but uninformative. Reason: Replace with the specific activity. Proposed replacements: citrate synthase activity Supporting Evidence: file:yeast/CIT2/CIT2-uniprot.txt Reaction=oxaloacetate + acetyl-CoA + H2O = citrate + CoA + H(+); |
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Download this section (compressed HTML)Q: Does Cit2p have physiologically relevant methylcitrate synthase activity, as suggested by the loss of all methylcitrate synthase activity in cit2 cit3 double mutants?
Citrate synthase, peroxisomal isozyme involved in glyoxylate cycle; catalyzes condensation of acetyl coenzyme A and oxaloacetate to form citrate; expression is controlled by Rtg1p and Rtg2p transcription factors; SCF-Ucc1 regulates level of Cit2p to maintain citrate homeostasis; oxaloacetate-dependent positive feedback loop inhibits Cit2p ubiquitination; CIT2 has a paralog, CIT1, that arose from the whole genome duplication
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