id: Q9I4X1
gene_symbol: pqsC
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:208964
  label: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM
    14847 / LMG 12228 / 1C / PRS 101 / PAO1)
description: >-
  PqsC (PA0998) is the catalytic subunit of the heterodimeric condensing enzyme
  PqsBC, which carries out the second step of 2-alkyl-4(1H)-quinolone (AQ/HAQ)
  biosynthesis in the Pseudomonas aeruginosa pqs quorum-sensing pathway. After
  PqsD generates 2-aminobenzoylacetate (2-ABA) from anthraniloyl-CoA and
  malonyl-CoA, PqsBC catalyzes the decarboxylative coupling of 2-ABA with an
  octanoyl group (from octanoyl-CoA) carried on PqsC to produce
  2-heptyl-4(1H)-quinolone (HHQ), the direct precursor of the Pseudomonas quinolone
  signal PQS (PMID:24239007). PqsC adopts a beta-ketoacyl-ACP synthase III
  (FabH/KAS III) fold but does not catalyze a fatty-acid synthase reaction; its
  reaction is EC 2.3.1.230 ("2-heptyl-4(1H)-quinolone synthase"), with an active
  site formed by Cys-129 and His-269 (PMID:26811339). The enzyme is an obligate
  heterodimer: PqsB is catalytically inactive but tightly associated and required
  for activity. The AQ signals it helps produce control biofilm development and
  numerous virulence factors, making PqsBC a target for anti-virulence drug
  development.
references:
- id: PMID:24239007
  title: 'The end of an old hypothesis: the pseudomonas signaling molecules 4-hydroxy-2-alkylquinolines
    derive from fatty acids, not 3-ketofatty acids.'
  findings:
  - statement: >-
      HAQ biosynthesis requires PqsABCD and proceeds in two steps; PqsBC carries out
      the second, condensing 2-ABA with an octanoate group carried on PqsC to form HHQ.
    supporting_text: >-
      HAQ biosynthesis, which requires the PqsABCD enzymes, proceeds by a two-step
      pathway: (1) PqsD mediates the synthesis of 2-aminobenzoylacetate (2-ABA) from
      anthraniloyl-coenzyme A (CoA) and malonyl-CoA, then (2) the decarboxylating
      coupling of 2-ABA to an octanoate group linked to PqsC produces HHQ, the direct
      precursor of PQS. PqsB is tightly associated with PqsC and required for the second step.
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified primary mechanistic paper establishing the PqsBC condensation
      step and that octanoate (a fatty acid), not a 3-ketofatty acid, is the precursor.
- id: PMID:26811339
  title: 'PqsBC, a Condensing Enzyme in the Biosynthesis of the Pseudomonas aeruginosa
    Quinolone Signal: CRYSTAL STRUCTURE, INHIBITION, AND REACTION MECHANISM.'
  findings:
  - statement: >-
      PqsBC is an obligate heterodimer; the catalytic active site (Cys-129, His-269)
      is contributed by PqsC.
    supporting_text: >-
      does not form a catalytic triad with His-269 and Cys-129, and in its place a valine (Val-299) is present
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Crystal structure (PDB 5DWZ); assigns the catalytic residues to PqsC and the
      EC 2.3.1.230 reaction to the PqsBC complex.
- id: PMID:12426334
  title: Functions required for extracellular quinolone signaling by Pseudomonas aeruginosa.
  findings:
  - statement: >-
      The pqsABCDE operon (including pqsC) is required for synthesis of the
      extracellular Pseudomonas quinolone signal.
    supporting_text: >-
      Functions required for extracellular quinolone signaling by Pseudomonas aeruginosa
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Genetic basis (IMP) for involvement of pqs genes in quinolone signal biosynthesis.
- id: file:PSEAE/pqsC/pqsC-notes.md
  title: pqsC review notes (BGC project) with predicted-complex evidence
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping
existing_annotations:
- term:
    id: GO:0044550
    label: secondary metabolite biosynthetic process
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: >-
      Phylogenetic (IBA) inference that PqsC participates in secondary metabolite
      biosynthesis. PqsC is the catalytic subunit of the PqsBC condensing enzyme
      that makes the alkylquinolone (HAQ) secondary metabolites, so this is correct.
    action: ACCEPT
    reason: >-
      Core biological process. HAQs/HHQ are secondary metabolites (quorum-sensing
      signals); PqsC is essential for their biosynthesis. Consistent with the
      experimental IMP annotation (PMID:12426334) below.
    supported_by:
    - reference_id: PMID:24239007
      supporting_text: >-
        HAQ biosynthesis, which requires the PqsABCD enzymes, proceeds by a two-step
        pathway
- term:
    id: GO:0004315
    label: 3-oxoacyl-[acyl-carrier-protein] synthase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: >-
      InterPro-based (IEA) assignment from the beta-ketoacyl-ACP synthase III
      (FabH/KAS III) signature. PqsC adopts this fold but does NOT catalyze the
      ACP-dependent Claisen condensation of fatty-acid synthesis; it catalyzes the
      decarboxylative coupling of 2-ABA with octanoyl-CoA to form HHQ (EC 2.3.1.230).
      The term is therefore wrong-specific.
    action: MODIFY
    reason: >-
      The fold-based prediction picks the wrong specific activity. The accurate
      activity is an acyl transfer (not a 3-oxoacyl-ACP/fatty-acid synthase reaction).
      Replace with the accurate parent GO:0016747 and propose a specific new term for
      EC 2.3.1.230 (see proposed_new_terms).
    proposed_replacement_terms:
    - id: GO:0016747
      label: acyltransferase activity, transferring groups other than amino-acyl groups
    supported_by:
    - reference_id: PMID:26811339
      supporting_text: >-
        does not form a catalytic triad with His-269 and Cys-129, and in its place a valine (Val-299) is present
    - reference_id: PMID:24239007
      supporting_text: >-
        the decarboxylating coupling of 2-ABA to an octanoate group linked to PqsC
        produces HHQ
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: >-
      Subcellular-location IEA. Consistent with the experimental cytoplasmic
      localization (EXP, PMID:24239007) below and with PqsBC being a soluble
      cytoplasmic condensing enzyme.
    action: ACCEPT
    reason: Correct cellular component; corroborated by experimental evidence.
- term:
    id: GO:0006633
    label: fatty acid biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  review:
    summary: >-
      InterPro-based (IEA) over-propagation from the KAS III (FabH) signature. PqsBC
      is not part of fatty-acid biosynthesis: an octanoyl group is a SUBSTRATE, and
      the PRODUCT is a quinolone quorum-sensing signal, not a fatty acid. Dulcey et
      al. (2013) explicitly established that HAQs derive from fatty acids rather than
      being made by a fatty-acid-synthase-type pathway.
    action: REMOVE
    reason: >-
      Demonstrably incorrect biological process. The enzyme consumes a fatty acyl
      substrate but synthesizes an alkylquinolone; assigning fatty acid biosynthesis
      is a domain-propagation error.
    supported_by:
    - reference_id: PMID:24239007
      supporting_text: >-
        the pseudomonas signaling molecules 4-hydroxy-2-alkylquinolines derive from
        fatty acids, not 3-ketofatty acids
- term:
    id: GO:0016746
    label: acyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: >-
      InterPro-based (IEA) general acyltransferase activity. This broad parent is
      accurate for PqsC: the EC 2.3.1.230 reaction transfers an octanoyl/acyl group
      in a decarboxylative condensation. It is correct but uninformative relative to
      the specific activity proposed in proposed_new_terms.
    action: ACCEPT
    reason: >-
      Correct general molecular function (true parent of the specific HHQ-synthase
      activity). Retained as an accurate, if non-specific, MF.
    supported_by:
    - reference_id: PMID:24239007
      supporting_text: >-
        the decarboxylating coupling of 2-ABA to an octanoate group linked to PqsC
        produces HHQ
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: EXP
  original_reference_id: PMID:24239007
  qualifier: located_in
  review:
    summary: >-
      Experimental cytoplasmic localization, consistent with PqsBC functioning as a
      soluble cytoplasmic condensing enzyme.
    action: ACCEPT
    reason: Experimentally supported cellular component.
- term:
    id: GO:0044550
    label: secondary metabolite biosynthetic process
  evidence_type: IMP
  original_reference_id: PMID:12426334
  qualifier: involved_in
  review:
    summary: >-
      Experimental (IMP) evidence that pqs genes are required for extracellular
      quinolone signal synthesis. PqsC is essential for HHQ/HAQ production.
    action: ACCEPT
    reason: >-
      Core biological process with direct experimental (mutant phenotype) support.
      This is the defining process for the gene.
    supported_by:
    - reference_id: PMID:12426334
      supporting_text: >-
        Functions required for extracellular quinolone signaling by Pseudomonas aeruginosa
core_functions:
- description: >-
    Catalytic subunit of the PqsBC condensing enzyme (EC 2.3.1.230,
    2-heptyl-4(1H)-quinolone synthase): catalyzes the decarboxylative coupling of
    2-aminobenzoylacetate (2-ABA) with an octanoyl group from octanoyl-CoA to form
    2-heptyl-4(1H)-quinolone (HHQ); active site Cys-129/His-269 (PMID:26811339). This
    is the essential biosynthetic step for the 2-alkyl-4(1H)-quinolone (HAQ)
    quorum-sensing signals (HHQ, the precursor of PQS) in the P. aeruginosa pqs pathway.
    GO currently lacks a specific MF term for this reaction (see proposed_new_terms).
  molecular_function:
    id: GO:0016747
    label: acyltransferase activity, transferring groups other than amino-acyl groups
  directly_involved_in:
    - id: GO:0044550
      label: secondary metabolite biosynthetic process
  supported_by:
  - reference_id: PMID:24239007
    supporting_text: >-
      the decarboxylating coupling of 2-ABA to an octanoate group linked to PqsC
      produces HHQ
proposed_new_terms:
- proposed_name: 2-heptyl-4(1H)-quinolone synthase activity
  proposed_definition: >-
    Catalysis of the reaction: (2-aminobenzoyl)acetate + octanoyl-CoA + H+ =
    2-heptyl-4(1H)-quinolone + CO2 + CoA. This decarboxylative condensation, carried
    out by the PqsBC heterodimer (catalytic subunit PqsC), is the penultimate step in
    Pseudomonas quinolone signal (PQS) biosynthesis.
  justification: >-
    EC 2.3.1.230 ("2-heptyl-4(1H)-quinolone synthase") has no corresponding GO
    molecular function term. The existing IEA annotation GO:0004315
    (3-oxoacyl-[acyl-carrier-protein] synthase activity) is a fold-based
    misassignment, and GO:0016747 (its proposed replacement) is only a general
    parent. A specific term would accurately capture the activity of PqsC/PqsBC.
suggested_questions:
- question: >-
    Per GO guidelines the 2-heptyl-4(1H)-quinolone synthase activity (EC 2.3.1.230) is
    annotated to the catalytic subunit PqsC (enables); should the required but
    non-catalytic PqsB additionally carry a contributes_to to reflect that the activity
    is realized only in the assembled PqsBC heterodimer?
suggested_experiments:
- description: >-
    Targeted active-site mutagenesis (Cys-129, His-269) coupled to in vitro HHQ
    synthase assays to formally delimit which steps require each residue, confirming
    the GO term boundary for the proposed 2-heptyl-4(1H)-quinolone synthase activity.