Class II poly(3-hydroxyalkanoate) synthase (PhaC-II/PhaC2) encoded in the phaC1-phaZ-phaC2-phaD locus of Pseudomonas putida KT2440. It polymerizes medium-chain-length (R)-3-hydroxyacyl-CoA substrates into intracellular PHA storage polyester and is one of two related synthases in the locus. Its relative contribution and substrate preferences compared with PhaC1 remain unresolved in native KT2440.
Definition: Catalysis of the transfer and polymerization of 3-hydroxyacyl groups from (R)-3-hydroxyacyl-CoA to a growing poly(3-hydroxyalkanoate) chain, releasing coenzyme A.
Justification: GO already contains process terms for poly(3-hydroxyalkanoate) biosynthesis, but it lacks the corresponding catalytic molecular-function term. This forces PHA polymerases such as PhaC-II/PhaC2 into the overly broad parent term acyltransferase activity.
Parent term: acyltransferase activity, transferring groups other than amino-acyl groups
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0016746 acyltransferase activity | IEA GO_REF:0000002 | MODIFY | Summary: The annotation captures the correct transferase chemistry, but GO:0016747 is a more informative child term for the non-amino-acyl hydroxyalkanoyl transfer catalyzed by PhaC2. Proposed replacements: acyltransferase activity, transferring groups other than amino-acyl groups Supporting Evidence: PMID:31468725 These CoA monomers can then be polymerized into mcl‐PHAs via the PHA synthases, PhaC1 and PhaC2 (Ren et al., 2009) file:PSEPK/phaC/phaC-deep-research-openai.md **PhaC2 is an enzyme that catalyzes the polymerization of (R)-3-hydroxyacyl-CoA monomers into PHA polyester** file:PSEPK/phaC/phaC-deep-research-falcon.md PhaC polymerases (including PhaC2) use **(R)-3-hydroxyacyl-CoA** substrates to synthesize intracellular PHA polyesters. This reaction is the committed polymerization step converting the soluble monomer pool into stored polymer. |
| GO:0042619 poly-hydroxybutyrate biosynthetic process | IEA GO_REF:0000002 | MODIFY | Summary: Too narrow for the KT2440 enzyme. Pseudomonas putida KT2440 is described as an mcl-PHA producer, and the relevant pathway literature places PhaC2 in poly(3-hydroxyalkanoate) polymerization rather than specifically poly-hydroxybutyrate synthesis. Falcon deep research reinforces this; it explicitly assigns PhaC2/PP_5005 to the class II PhaC family that produces medium-chain-length (C6-C14) PHA in pseudomonads, and notes the protein is granule-associated rather than a PHB (scl-PHA) synthase. Replace with the existing broader GO term for poly(3-hydroxyalkanoate) biosynthesis. Proposed replacements: poly(3-hydroxyalkanoate) biosynthetic process Supporting Evidence: PMID:31468725 Among these Pseudomonads, Pseudomonas putida KT2440 naturally produces mcl‐PHAs as a carbon storage compound in scenarios of carbon excess and nutrient limitation (de Eugenio et al., 2010) PMID:31468725 These CoA monomers can then be polymerized into mcl‐PHAs via the PHA synthases, PhaC1 and PhaC2 (Ren et al., 2009) file:PSEPK/phaC/phaC-deep-research-falcon.md KT2440 is described as producing **medium-chain-length PHA copolymers** with monomers **ranging from C6 to C14** depending on carbon source. file:PSEPK/phaC/phaC-deep-research-falcon.md The retrieved KT2440 literature consistently places PhaC2 in the **class II PhaC** family responsible for **mcl-PHA** production in pseudomonads, which is consistent with UniProt’s functional description “poly(3-hydroxyalkanoate) polymerase” |
| GO:0070088 polyhydroxyalkanoate granule | ISS PMID:20937103 Influence of growth stage on activities of polyhydroxyalkano... | NEW | Summary: Class II PhaC polymerases act as granule-associated enzymes in characterized Pseudomonas mcl-PHA systems. Reason: PhaC2 belongs to the same class II polymerase system, but no direct KT2440 PhaC2 localization assay was identified, so ISS is appropriate rather than IDA. Supporting Evidence: PMID:38608840 although PhaI, PhaC, and PhaZ are all located on the PHA granule and involved in PHA metabolism PMID:20937103 These granule-associated proteins include PHA polymerases (PhaC), PHA depolymerase (PhaZ) [9-11], phasins (PhaF and PhaI) [7,12,13] and acyl-CoA synthetase [14]. |
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Download this section (compressed HTML)Q: Under which carbon sources or stress states does PhaC-II make a distinct contribution relative to PhaC1 in the native KT2440 background?
Suggested experts: Pseudomonas PHA metabolism researchers
Q: Does PhaC-II primarily affect polymer composition or granule architecture rather than total PHA yield in KT2440?
Suggested experts: PHA enzyme biochemists
Q: Is PhaC-II preferentially associated with a specific subset of PHA granules or a specific phase of granule maturation?
Suggested experts: Bacterial cell biology and granule biogenesis researchers
Experiment: Construct clean single-polymerase KT2440 strains and complementation series for phaC1 and phaC-II, then compare PHA yield and monomer composition across gluconate, fatty acids, and aromatic substrates.
Hypothesis: PhaC-II contributes condition-specific polymerization activity that is masked in the wild-type dual-synthase background.
Type: genetics and metabolite/polymer phenotyping
Experiment: Purify KT2440 PhaC-II and measure polymerization activity against a panel of R-3-hydroxyacyl-CoA substrates spanning short- to medium-chain monomers.
Hypothesis: KT2440 PhaC-II has a substrate range biased toward medium-chain R-3-hydroxyacyl-CoA substrates and may differ measurably from PhaC1 in chain-length preference.
Type: biochemical enzyme assay
Experiment: Tag PhaC1 and PhaC-II separately and compare granule association by fluorescence microscopy or granule proteomics during PHA accumulation.
Hypothesis: PhaC-II has a distinct role in granule nucleation or granule occupancy during nitrogen-limited PHA accumulation.
Type: cell biology and proteomics
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