PvdQ (PA2385) is a periplasmic N-terminal nucleophile (Ntn) hydrolase of the peptidase S45 (penicillin acylase) family. It is made as a precursor with a signal peptide and matures autoproteolytically into an alpha/beta heterodimer whose beta-subunit N-terminal serine is the nucleophile. It is an acyl-homoserine lactone (AHL) acylase (EC 3.5.1.97) that removes the fatty acyl chain from long-chain AHLs (11 to 14 carbons), including the Las quorum-sensing signal 3-oxo-C12-HSL, releasing homoserine lactone and the free fatty acid, and so has quorum-quenching activity. Its main physiological role is in pyoverdine siderophore biosynthesis: expressed under iron starvation, it removes a fatty acyl chain from the acylated pyoverdine precursor in the periplasm, a maturation step needed to make mature pyoverdine. Loss of pvdQ abolishes pyoverdine production and, under iron limitation, reduces swarming, biofilm formation and virulence.
Definition: Catalysis of the reaction an N-acyl-L-homoserine lactone + H2O = L-homoserine lactone + a carboxylate (EC 3.5.1.97, RHEA:18937).
Justification: GO has an AHL synthase term (GO:0061579) but no term for AHL acylase (EC 3.5.1.97). PvdQ, QuiP and PA0305 (HacB) of P. aeruginosa all have this activity shown directly, and the closest available term is the generic GO:0016811.
Parent term: hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0002049 pyoverdine biosynthetic process | IDA PMID:22498339 High cellular organization of pyoverdine biosynthesis in Pse... | ACCEPT | Summary: PvdQ catalyses the periplasmic deacylation of the acyl-pyoverdine precursor, a step of pyoverdine biosynthesis. The cited paper is a localization study (abstract only); the process claim is correct and agrees with the other pyoverdine rows. Reason: Direct catalytic participation in pyoverdine maturation, supported across several papers. The IDA code on a localization paper is generous, but the claim is sound and consistent with the IMP rows. Supporting Evidence: PMID:22498339 PvdQ, involved in the maturation of PVDI in the periplasm PMID:21892836 Structural studies are also presented showing PvdQ covalently acylated with the acyl moiety substrate derived from the acyl-pyoverdine precursor |
| GO:0002049 pyoverdine biosynthetic process | IMP PMID:12686626 Identification and characterization of novel pyoverdine synt... | ACCEPT | Summary: pvdQ mutant identified as required for pyoverdine synthesis. Reason: Core process; PvdQ performs the deacylation maturation step. Supporting Evidence: PMID:12686626 Eight new pvd genes were identified. |
| GO:0002049 pyoverdine biosynthetic process | IMP PMID:19787431 Synthesis of the siderophore pyoverdine in Pseudomonas aerug... | ACCEPT | Summary: pvdQ mutant accumulates a periplasmic precursor and secretes an altered siderophore. Reason: Core process; the mutant phenotype places PvdQ in periplasmic maturation. Supporting Evidence: PMID:19787431 suggesting a role for PvdQ in the periplasmic maturation of PVDI |
| GO:0002049 pyoverdine biosynthetic process | IMP PMID:21892836 Structural characterization and high-throughput screening of... | ACCEPT | Summary: Structural and inhibitor work links PvdQ to deacylation of the acyl-pyoverdine precursor. Reason: Core process with mechanistic support. Supporting Evidence: PMID:21892836 Structural studies are also presented showing PvdQ covalently acylated with the acyl moiety substrate derived from the acyl-pyoverdine precursor |
| GO:0005737 cytoplasm | IDA PMID:22498339 High cellular organization of pyoverdine biosynthesis in Pse... | REMOVE | Summary: The cited abstract states that labelled PvdQ is uniformly distributed in the periplasm; the cytoplasmic and membrane enzyme in that paper is PvdA. PvdQ has an experimentally confirmed signal peptide. Reason: Contradicted by the cited paper itself. The correct location from this paper is GO:0042597 periplasmic space, which the gene already carries. Supporting Evidence: PMID:22498339 Epifluorescence and TIRF imaging on cells expressing labelled PvdQ showed that this enzyme was uniformly distributed in the periplasm |
| GO:0016787 hydrolase activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: True but uninformative; GO:0016811, accepted below, is a descendant. Reason: GO:0016811 is_a GO:0016810 is_a GO:0016787 and is accepted in this review. |
| GO:0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the PTN002151232 IBD, seeded by the three PAO1 AHL acylases PvdQ, QuiP and PA0305 (HacB). PvdQ's own IDA is one of the seeds, which is expected and not circular. All three seeds have direct activity evidence. Reason: Sound IBD; GO:0016811 is the most specific existing GO term for AHL acylase (EC 3.5.1.97 has no GO class) and suits a 21-leaf Ntn acylase clade. Supporting Evidence: PMID:16495538 In a bioassay, the purified acylase was shown to degrade AHLs with side chains ranging in length from 11 to 14 carbons at physiologically relevant low concentrations. |
| GO:0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides | IDA PMID:16495538 Quorum quenching by an N-acyl-homoserine lactone acylase fro... | ACCEPT | Summary: PseudoCAP IDA seed of PTN002151232. Purified PvdQ deacylates long-chain AHLs, releasing HSL and the fatty acid (full text read). Reason: Direct purified-enzyme evidence; the term is the most specific available for AHL acylase. Supporting Evidence: PMID:16495538 one can conclude that the PA2385 protein is an AHL acylase |
| GO:0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from the Pen/GL7ACA/AHL acylase signatures; agrees with the experimental rows. Reason: Consistent with the IDA and IBA rows on the same term. Supporting Evidence: PMID:16495538 one can conclude that the PA2385 protein is an AHL acylase |
| GO:0017000 antibiotic biosynthetic process | IEA GO_REF:0000002 | REMOVE | Summary: InterPro2GO mapping from the peptidase S45 signature (IPR002692), reflecting the industrial use of penicillin acylases to make semisynthetic beta-lactams. PvdQ shows no beta-lactam acylase activity and makes no antibiotic. Reason: Wrong for this gene. The purified-enzyme extract had no activity on the beta-lactams tested, and its biosynthetic role is in a siderophore, not an antibiotic. Supporting Evidence: PMID:16495538 No activity was detected. |
| GO:0042597 periplasmic space | IEA GO_REF:0000044 | ACCEPT | Summary: Periplasmic location is shown by imaging of labelled PvdQ and fits its signal peptide. Reason: Experimentally supported location where the maturation step occurs. Supporting Evidence: PMID:22498339 Epifluorescence and TIRF imaging on cells expressing labelled PvdQ showed that this enzyme was uniformly distributed in the periplasm |
| GO:0042802 identical protein binding | IPI PMID:20080736 The quorum-quenching N-acyl homoserine lactone acylase PvdQ ... | KEEP AS NON CORE | Summary: IntAct self-interaction from the structural work; reflects the alpha/beta heterodimer formed from one precursor, not a functional binding activity. Reason: Structurally true but not informative about function. Supporting Evidence: PMID:20080736 PvdQ has a typical alpha/beta heterodimeric Ntn-hydrolase fold |
| GO:0044010 single-species biofilm formation | IMP PMID:19778968 Role of PvdQ in Pseudomonas aeruginosa virulence under iron-... | MARK AS OVER ANNOTATED | Summary: The biofilm defect of the deletion mutant under iron limitation is attributed by the authors to the pyoverdine pathway. Reason: Indirect pleiotropic consequence of pyoverdine (iron) deficiency, not a process PvdQ performs. Supporting Evidence: PMID:19778968 PvdQ plays a major role in swarming motility, in biofilm development and in infection that is more likely to be linked to the pyoverdine pathway |
| GO:0046677 response to antibiotic | IMP PMID:21833667 Influence of Pseudomonas aeruginosa pvdQ gene on altering an... | MARK AS OVER ANNOTATED | Summary: Overexpression raises resistance under swarming conditions, which the authors relate to swarm-cell differentiation. Reason: Indirect phenotype; PvdQ has no known role in sensing or responding to antibiotics. Supporting Evidence: PMID:21833667 pvdQ plays an important role in elevating antibiotic resistance via swarm-cell differentiation and possibly other mechanisms as well |
| GO:0071978 bacterial-type flagellum-dependent swarming motility | IEP PMID:18245294 Swarming of Pseudomonas aeruginosa is a complex adaptation l... | MARK AS OVER ANNOTATED | Summary: pvdQ transcripts rise in swarming cells; expression change does not show involvement. Reason: Consistent with the IMP row on the same term; swarming requires PvdQ only indirectly. Supporting Evidence: PMID:18245294 two virulence genes, lasB and pvdQ , were required for swarming motility |
| GO:0071978 bacterial-type flagellum-dependent swarming motility | IMP PMID:18245294 Swarming of Pseudomonas aeruginosa is a complex adaptation l... | MARK AS OVER ANNOTATED | Summary: A PA14 pvdQ mutant swarms poorly (also seen in PAO1 under iron limitation), attributed to altered AHL signal or pyoverdine levels. Reason: Indirect phenotype via quorum signal or siderophore levels; PvdQ is not part of the motility machinery. Supporting Evidence: PMID:18245294 two virulence genes, lasB and pvdQ , were required for swarming motility |
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Download this section (compressed HTML)Q: Is AHL quorum quenching a physiological role of PvdQ, given that it is expressed mainly under iron starvation and that its in vivo phenotypes track pyoverdine rather than AHL levels?
Experiment: Compare kcat/Km of purified PvdQ for the acyl-pyoverdine precursor and for 3-oxo-C12-HSL to establish which is the physiological substrate.
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