UbiE (PA5063) is a bifunctional SAM-dependent C-methyltransferase that catalyzes the penultimate C-methylation step in both ubiquinone and menaquinone biosynthesis in P. aeruginosa. In the ubiquinone pathway, it converts 2-polyprenyl-6-methoxy-1,4-benzoquinol to 2-polyprenyl-3-methyl-6-methoxy-1,4-benzoquinol (EC 2.1.1.201); in the menaquinone pathway, it converts demethylmenaquinol to menaquinol (EC 2.1.1.163). Both ubiquinone-9 and menaquinone are essential electron carriers in the branched respiratory chain of P. aeruginosa, supporting aerobic respiration and anaerobic denitrification (PMID:32409583). The enzyme belongs to the class I SAM-binding methyltransferase superfamily (UbiE/COQ5 family). No direct experimental characterization exists in P. aeruginosa; function is inferred from orthologs in E. coli (PMID:9045837), S. cerevisiae COQ5 (PMID:9083049), and mycobacterial MenG (PMID:36417754).
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0006744 ubiquinone biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: IBA annotation for ubiquinone biosynthetic process, inferred from phylogenetic trees. UbiE catalyzes the C-methylation of 2-polyprenyl-6-methoxy-1,4-benzoquinol in the ubiquinone pathway. This is a core function of the UbiE/COQ5 family, well established in E. coli (PMID:9045837) and yeast (PMID:9083049). Reason: Core biosynthetic process. UbiE is directly involved in ubiquinone biosynthesis as the C-methyltransferase for the penultimate step. The BioReason SFT trace (ubiE-deep-research-bioreason-sft.md) also identifies menaquinone headgroup maturation as a core function, consistent with this annotation. Supporting Evidence: PMID:9045837 Strains of Escherichia coli with mutations in the ubiE gene are not able to catalyze the carbon methylation reaction in the biosynthesis of ubiquinone (coenzyme Q) and menaquinone (vitamin K2), essential isoprenoid quinone components of the respiratory electron transport chain file:PSEAE/ubiE/ubiE-deep-research-bioreason-sft.md A SAM-dependent C-methyltransferase in Pseudomonas aeruginosa that installs the C-3 methyl group on demethylated menaquinone (and related demethylated quinone intermediates), thereby advancing menaquinone headgroup maturation |
| GO:0008425 2-methoxy-6-polyprenyl-1,4-benzoquinol methyltransferase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA annotation for the specific molecular function in the ubiquinone pathway (EC 2.1.1.201). This is one of the two core catalytic activities of UbiE, converting DDMQH2 to DMQH2 via SAM-dependent C-methylation. Well supported by ortholog data from E. coli and yeast COQ5. Reason: Core molecular function. This is one of the two specific methyltransferase activities of UbiE, directly corresponding to EC 2.1.1.201. Supporting Evidence: PMID:9083049 Coq5p is required for the C-methyltransferase step that converts 2-methoxy-6-polyprenyl-1, 4-benzoquinone to 2-methoxy-5-methyl-6-polyprenyl-1,4-benzoquinone |
| GO:0006744 ubiquinone biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: IEA annotation for ubiquinone biosynthetic process from UniRule/UniPathway. Redundant with the IBA annotation above but independently supported. Correct annotation for a core biosynthetic function. Reason: Correct and redundant with phylogenetic inference. UniRule UR000030800 (HAMAP MF_01813) appropriately assigns this term to the UbiE/COQ5 family. |
| GO:0008168 methyltransferase activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO annotation from IPR004033 (UbiE/COQ5 methyltransferase) and IPR023576 (conserved site). The general methyltransferase activity term is correct but overly broad. More specific terms (GO:0008425 and GO:0043770) are already annotated and better represent the actual catalytic activities. Reason: Correct but too general. The more specific terms GO:0008425 (2-methoxy-6-polyprenyl-1,4-benzoquinol methyltransferase activity) and GO:0043770 (demethylmenaquinone methyltransferase activity) are already present and more informative. |
| GO:0008425 2-methoxy-6-polyprenyl-1,4-benzoquinol methyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: IEA annotation for the ubiquinone-pathway methyltransferase activity from UniRule. Correct and specific, corresponding to EC 2.1.1.201. Redundant with the IBA annotation. Reason: Correct specific molecular function. Independently supported by both UniRule/Rhea and phylogenetic inference. |
| GO:0009060 aerobic respiration | IEA GO_REF:0000104 | KEEP AS NON CORE | Summary: IEA annotation for aerobic respiration. Ubiquinone is indispensable for the aerobic electron transport chain in P. aeruginosa (PMID:6774977), so ubiE is required for aerobic respiration. However, this is an indirect downstream consequence of ubiquinone biosynthesis rather than a direct function of ubiE. The enzyme catalyzes a biosynthetic step; it does not directly participate in electron transport. Reason: While correct that UbiE activity is required for aerobic respiration (because ubiquinone is essential for the respiratory chain), this annotation describes a downstream physiological consequence rather than the direct molecular role. The core annotation is the biosynthetic process. Supporting Evidence: PMID:6774977 Complete removal of ubiquinone performed by extracting the lyophilized membrane particles with n-pentane containing acetone resulted in complete loss of all oxidase activities for glucose, gluconate, malate, succinate, and NADH |
| GO:0009234 menaquinone biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: IEA annotation for menaquinone biosynthetic process from UniRule/UniPathway. UbiE catalyzes the final step in menaquinone headgroup maturation, converting demethylmenaquinol to menaquinol. This is the second of the two core biosynthetic pathways involving UbiE. Reason: Core biosynthetic process. UbiE/MenG directly catalyzes the terminal C-methylation step in menaquinone biosynthesis, well established in E. coli and mycobacteria. Supporting Evidence: PMID:9045837 Strains of Escherichia coli with mutations in the ubiE gene are not able to catalyze the carbon methylation reaction in the biosynthesis of ubiquinone (coenzyme Q) and menaquinone (vitamin K2), essential isoprenoid quinone components of the respiratory electron transport chain |
| GO:0042181 ketone biosynthetic process | IEA GO_REF:0000117 | MARK AS OVER ANNOTATED | Summary: ARBA-assigned annotation for ketone biosynthetic process. Ubiquinone and menaquinone are quinones (not ketones per se, although quinones contain carbonyl groups). This is an overly general and somewhat misleading parent term. The specific pathway terms (GO:0006744 ubiquinone biosynthetic process and GO:0009234 menaquinone biosynthetic process) are already present and far more informative. Reason: Technically not wrong (quinones contain ketone-like carbonyl groups), but this is an uninformative high-level grouping term that obscures the actual biology. The specific quinone biosynthesis terms already capture the biology precisely. |
| GO:0043770 demethylmenaquinone methyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: IEA annotation for the menaquinone-pathway methyltransferase activity (EC 2.1.1.163) from UniRule. This is the second of the two core catalytic activities of UbiE, converting demethylmenaquinol to menaquinol. Well supported by ortholog data, including direct enzymatic characterization of mycobacterial MenG (PMID:36417754). Reason: Core molecular function. This is the specific methyltransferase activity for the menaquinone pathway, directly corresponding to EC 2.1.1.163. Supporting Evidence: PMID:36417754 Partially purified recombinant protein catalyzed the formation of MK from demethylmenaquinone (DMK), although the activity of the recombinant protein was low and appeared to require a cofactor or intact membrane structure for activity |
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Download this section (compressed HTML)Q: Does P. aeruginosa ubiE have a preference for the ubiquinone versus menaquinone pathway substrate? The relative importance of each pathway may differ from E. coli given that UQ9 is the dominant quinone in P. aeruginosa.
Suggested experts: Fabien Pierrel, Ludovic Pelosi
Q: Is there any direct experimental evidence for ubiE function in P. aeruginosa (e.g., gene knockout, complementation, or enzymatic assay)?
Experiment: Generate a clean deletion of PA5063 (ubiE) in P. aeruginosa PAO1 using allelic exchange. Assess growth phenotype on aerobic and anaerobic (denitrifying) media. Analyze quinone profiles (UQ9, MK, DMK) by HPLC-MS. Complement with wild-type ubiE expressed from a plasmid.
Hypothesis: P. aeruginosa ubiE knockout would be deficient in both ubiquinone and menaquinone biosynthesis, resulting in growth defects under both aerobic and anaerobic conditions.
Type: gene knockout and metabolite profiling
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