PA2634 (aceA) encodes the isocitrate lyase (ICL) of Pseudomonas aeruginosa, the first enzyme of the glyoxylate shunt. ICL cleaves isocitrate into succinate and glyoxylate, so that, together with malate synthase, acetyl-CoA can be assimilated without the carbon losses of the oxidative TCA steps. The PAO1 enzyme is a 531-residue member of the isocitrate lyase/PEP mutase superfamily, closer to the ICL of Colwellia maris than to those of other pseudomonads; its crystal structure is solved (PDB 6G1O). ICL is induced by acetate, citronellol and leucine and repressed by glucose or citrate, and aceA is required for growth on acetate, on acyclic monoterpenes of the citronellol family, on alkanols and on leucine, all of which are catabolised to acetyl-CoA. Under oxygen limitation aceA mutants also show reduced type III secretion and increased biofilm formation, effects attributed to altered central metabolism.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: Root catalytic activity from the ICL/PEPM superfamily InterPro entry. Reason: Entailed by the isocitrate lyase activity accepted in this review. |
| GO:0004451 isocitrate lyase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Isocitrate lyase activity by IBA from PTN000493043 (9 seeds). Reason: The node is seeded by characterised isocitrate lyases from E. coli (AceA, P0A9G6), M. tuberculosis, yeast, Candida, Arabidopsis and rice, as well as by this gene's own PseudoCAP IDA, which is expected and not circular. PA2634 keeps the ICL family signature and the active-site and substrate-binding residues, so it lies inside the clade that has the activity. Supporting Evidence: file:PSEAE/PA2634/PA2634-uniprot.txt IPR006254; Isocitrate_lyase. PMID:17319879 Genetic complementation further confirmed that the aceA gene encodes the ICL enzyme. |
| GO:0004451 isocitrate lyase activity | IDA PMID:17319879 Identification of the aceA gene encoding isocitrate lyase re... | ACCEPT | Summary: PseudoCAP IDA, one of nine seeds of the PTN000493043 IBD. ICL activity was measured in crude extracts of PAO1 grown on acetate, citronellol or leucine, the 60-kDa ICL band was seen only in acetate-grown cells, and complementation of the transposon mutant confirmed that aceA encodes the enzyme. Reason: Abstract only. Activity in wild-type extracts combined with a complemented mutant ties the ICL activity to PA2634, and the protein carries the complete ICL family signature. Seed verdict SOUND. The direct part of the evidence is a crude-extract assay rather than a purified enzyme, so IMP plus IDA would describe it more exactly, but the term is right for the gene. Supporting Evidence: PMID:17319879 The ICL enzyme activity in crude extracts from cultures of the PAO1 strain was induced by acetate, citronellol and leucine, and repressed by growth on glucose or citrate. PMID:17319879 Genetic complementation further confirmed that the aceA gene encodes the ICL enzyme. |
| GO:0004451 isocitrate lyase activity | IEA GO_REF:0000120 | ACCEPT | Summary: EC 4.1.3.1 / Rhea / InterPro mapping; consistent with the experimental row. Reason: Same claim as the IDA and IBA rows. Supporting Evidence: PMID:17319879 Genetic complementation further confirmed that the aceA gene encodes the ICL enzyme. |
| GO:0004451 isocitrate lyase activity | ISS GO_REF:0000024 | ACCEPT | Summary: ISS from E. coli AceA by UniProt curators; consistent with the experimental row. Reason: The E. coli enzyme is the characterised reference ICL; same claim as the IDA row. Supporting Evidence: PMID:17319879 Genetic complementation further confirmed that the aceA gene encodes the ICL enzyme. |
| GO:0006097 glyoxylate cycle | IBA GO_REF:0000033 | ACCEPT | Summary: Glyoxylate cycle by IBA from PTN000493043. Reason: ICL catalyses the first committed step of the glyoxylate shunt; the seeds are characterised ICLs. The P. aeruginosa paper concludes that acetyl-CoA from acetate, terpene and leucine catabolism is channelled into the shunt through this enzyme. Supporting Evidence: PMID:17319879 These results suggest that ICL is involved in the assimilation of acetate, acyclic monoterpenes of the citronellol family, alkanols, and leucine, in which the final intermediary acetyl-coenzyme A may be channelled to the glyoxylate shunt. |
| GO:0006097 glyoxylate cycle | IEA GO_REF:0000041 | ACCEPT | Summary: UniPathway mapping to the glyoxylate cycle; same claim as the IBA row. Reason: Consistent with the IBA and with the growth requirement on acetate. Supporting Evidence: file:PSEAE/PA2634/PA2634-uniprot.txt Carbohydrate metabolism; glyoxylate cycle; (S)-malate from isocitrate |
| GO:1900232 negative regulation of single-species biofilm formation on inanimate substrate | IMP PMID:23363478 Type III secretion system expression in oxygen-limited Pseud... | MARK AS OVER ANNOTATED | Summary: PseudoCAP IMP. An aceA mutant formed more biofilm under anaerobic conditions, complemented in trans, with higher pslA transcript levels. Not an IBD seed. Reason: Full text read. The phenotype is real, but it is shared by other central-metabolism mutants in the same experiment (aceE, aceK, icd-idh, glcB), so it reflects altered metabolic state rather than a regulatory activity of the ICL protein. The authors themselves propose an indirect route through the RetS/LadS signalling pathway. ICL catalyses a metabolic step; it is not shown to take part in regulating biofilm formation. Supporting Evidence: PMID:23363478 Biofilm formation under anaerobic conditions was significantly enhanced in the aceA mutant as well as in the other mutants that showed reduced PcrV expression PMID:23363478 An aceA mutant displayed enhanced biofilm formation during anaerobic growth, which suggested that AceA-dependent modulation of type III secretion might impinge upon the RetS/LadS signalling pathways. |
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Download this section (compressed HTML)Q: Is the effect of aceA loss on type III secretion and biofilm formation under oxygen limitation a consequence of glyoxylate or succinate levels, or of carbon flux elsewhere in central metabolism?
Experiment: Compare an aceA deletion with a catalytically dead ICL point mutant (active-site Cys) for T3SS expression and anaerobic biofilm formation, to separate enzymatic and non-enzymatic contributions.
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