Bacterial medium-chain-length PHA synthesis and mobilization

A reusable bacterial module for production and intracellular turnover of medium-chain-length poly(3-hydroxyalkanoate) storage polyester. The required core begins with an externally supplied (R)-3-hydroxyacyl-CoA pool: class II PhaC enzymes polymerize these monomers at PHA granules, and intracellular PhaZ depolymerases remobilize stored polymer. PhaG-dependent routing from de novo fatty-acid synthesis is an optional upstream submodule whose physiological chemistry is not fixed here. Beta-oxidation-derived monomer supply and phasin-mediated granule organization are adjacent processes outside the core reaction boundary.

MODULE:bacterial_mcl_pha_synthesis_and_mobilizationDRAFTCONCRETEMetabolic Pathwaymodules/bacterial_mcl_pha_synthesis_and_mobilization.yaml
poly(3-hydroxyalkanoate) metabolic processGO:0042620
PMID:9727022
A new metabolic link between fatty acid de novo synthesis and polyhydroxyalkanoic acid synthesis. The PHAG gene from Pseudomonas putida KT2440 encodes a 3-hydroxyacyl-acyl carrier protein-coenzyme a transferase.
Genetic complementation and purified-protein assays establish PhaG as an optional link between de novo fatty-acid synthesis and PHA precursor supply.
PMID:17137299
Metabolic engineering and characterization of phaC1 and phaC2 genes from Pseudomonas putida KCTC1639 for overproduction of medium-chain-length polyhydroxyalkanoate.
Overexpression experiments give distinct PhaC1 and PhaC2 phenotypes and support representing them as nonsequential class II polymerase-family members.
PMID:20937103
Influence of growth stage on activities of polyhydroxyalkanoate (PHA) polymerase and PHA depolymerase in Pseudomonas putida U.
Pseudomonas PhaC polymerase and PhaZ depolymerase are granule-associated activities that can operate concomitantly during intracellular PHA turnover.
PMID:17170116
Biochemical evidence that phaZ gene encodes a specific intracellular medium chain length polyhydroxyalkanoate depolymerase in Pseudomonas putida KT2442: characterization of a paradigmatic enzyme.
Purified PhaZ is an intracellular, PHA-granule-localized depolymerase that hydrolyzes medium-chain-length PHA containing aliphatic and aromatic monomers.
file:PSEPK/phaG/phaG-ai-review.yaml
PSEPK phaG gene review
The curated O85207 review supports the fatty-acid-synthesis bridge that supplies medium-chain (R)-3-hydroxyacyl units for PHA synthesis.
file:projects/P_PUTIDA/deep-research/PSEPK__mcl_pha_monomer_supply_from_fas__upa00212-deep-research-openscientist.md
OpenScientist UPA00212 module, pathway, and PSEPK taxon review
Establishes PhaG-dependent routing as a genuine but mechanistically unresolved optional route and identifies a possible separate PP_0763 CoA-activation step under the two-enzyme model.
file:modules/mcl_pha_monomer_supply_from_fas-deep-research-openscientist.md
OpenScientist generic PhaG monomer-supply module review
Reviews the competing direct-transacylase and thioesterase-plus-ligase models and the alternative beta-oxidation-derived supply route.
file:PSEPK/phaC/phaC-deep-research-openscientist.md
OpenScientist PSEPK PhaC2 review
Supports class II mcl-PHA synthase assignment while leaving the native PhaC1/PhaC2 division of labor unresolved.
file:PSEPK/phaZ/phaZ-deep-research-openscientist.md
OpenScientist PSEPK PhaZ review
Supports intracellular granule-associated mcl-PHA depolymerase activity and rejects the generic glycerolipid annotations.
file:PSEPK/phaA/phaA-ai-review.yaml
PSEPK phaC1 gene review
The curated Q88D25 review identifies PhaC1 as one of the two class II polymerases and places it at the polyhydroxyalkanoate granule.
file:PSEPK/phaC/phaC-ai-review.yaml
PSEPK phaC2 gene review
The curated Q88D23 review supports a second class II polymerase that contributes under condition-dependent PHA-producing states.
file:PSEPK/phaZ/phaZ-ai-review.yaml
PSEPK phaZ gene review
The curated Q88D24 review supports intracellular granule-associated depolymerization of medium-chain-length PHA.

PhaC1 and PhaC2 are represented as members of one class II synthase family, not as sequential steps. The core module is complete from an (R)-3-hydroxyacyl-CoA input boundary through polymerization and mobilization. PhaG is optional upstream context because beta-oxidation and other routes can independently provide PhaC substrates; its in vivo chemistry is deliberately not asserted as a single direct ACP:CoA reaction. The PhaG annoton therefore records a routing role without assigning substrates, products, or a module-level catalytic function. A thioesterase-plus-ligase model implicating PP_0763 remains plausible but is not promoted to a required step without direct native-context resolution. PhaC1 and PhaC2 are co-exemplars of one class II synthase role; neither is labeled primary, redundant, or substrate-specialized. PhaF, PhaI, and PhaD affect granule architecture or regulation but do not define additional reaction steps in this module.

4Nodes
3Parts
0Variant Sets
0Variants
3Annotons
2Connections

Derived QC

Recommended-field compliance

7.7% recommended fields populated
  • module.knowledge_gaps[0] · boundary (0/1)
  • module.knowledge_gaps[0] · gap_kind (0/1)
  • module.knowledge_gaps[0] · status (0/1)
  • module.knowledge_gaps[0] · provenance (0/1)
  • module.knowledge_gaps[1] · boundary (0/1)
  • module.knowledge_gaps[1] · gap_kind (0/1)
  • module.knowledge_gaps[1] · status (0/1)
  • module.knowledge_gaps[1] · provenance (0/1)
  • module.knowledge_gaps[2] · boundary (0/1)
  • module.knowledge_gaps[2] · gap_kind (0/1)
  • module.knowledge_gaps[2] · status (0/1)
  • module.knowledge_gaps[2] · provenance (0/1)

Module deep research

✗ none found

No MODULE:bacterial_mcl_pha_synthesis_and_mobilization deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Gene-review completeness (4/9 grounded genes reviewed)

4 complete review(s) · 4 with deep research · 5 missing review · 0 reviewed but lacking deep research

Gene Review Complete Deep research
Ectopseudomonas oleovorans PhaC1 P26494 ✗ — —
Ectopseudomonas oleovorans PhaZ P26495 ✗ — —
Ectopseudomonas oleovorans PhaC2 P26496 ✗ — —
phaA Q88D25 ✓ ✓ ✓
phaC Q88D23 ✓ ✓ ✓
phaG O85207 ✓ ✓ ✓
phaZ Q88D24 ✓ ✓ ✓
Pseudomonas aeruginosa PhaG Q51553 ✗ — —
Ectopseudomonas oleovorans PhaG Q9KJH8 ✗ — —

Details

Context
bacteriaNCBITaxon:2
Bacterial medium-chain-length PHA synthesis and mobilizationMetabolic Pathwaybacterial_mcl_pha_synthesis_and_mobilization
poly(3-hydroxyalkanoate) metabolic processGO:0042620
Context
bacteriaNCBITaxon:2

Connections

PhaG-dependent routing can feed the external (R)-3-hydroxyacyl-CoA pool consumed by class II PhaC, potentially through a separate CoA-activation step.
The PhaC-produced intracellular PHA polymer is the substrate mobilized by PhaZ.
Part 1: optional fatty-acid-synthesis-derived monomer routing (optional)
PhaG-mediated mcl-PHA monomer supplyMetabolic Pathwaypha_monomer_supply_from_fas

Annotons

PhaG-dependent 3-hydroxyacyl routing
phag_monomer_supply
Participant: Family: experimentally supported PhaG ortholog family
Family:
experimentally supported PhaG ortholog family
Representative Members: PSEPK PhaGUniProtKB:O85207 Pseudomonas aeruginosa PhaGUniProtKB:Q51553 Ectopseudomonas oleovorans PhaGUniProtKB:Q9KJH8

Processes

poly(3-hydroxyalkanoate) biosynthetic processGO:0042621

Routes medium-chain (R)-3-hydroxyacyl units from de novo fatty-acid synthesis toward PHA production. Purified PhaG shows acyltransferase activity, but this module does not choose between direct ACP:CoA transacylation and hydrolysis followed by a separate CoA-activation step in vivo.

Part 2: medium-chain-length PHA polymerization
Class II PhaC polymerizationReactionmcl_pha_polymerization

Annotons

Class II poly(3-hydroxyalkanoate) polymerase
class_ii_phac_polymerase
Participant: Family: class II PHA synthase family
Family:
class II PHA synthase familyInterPro:IPR011287
Representative Members: PSEPK PhaC1UniProtKB:Q88D25 PSEPK PhaC2UniProtKB:Q88D23 Ectopseudomonas oleovorans PhaC1UniProtKB:P26494 Ectopseudomonas oleovorans PhaC2UniProtKB:P26496
Required Function:
acyltransferase activity, transferring groups other than amino-acyl groupsGO:0016747

Function

medium-chain-length poly(3-hydroxyalkanoate) polymerizationGO:0016747
Substrates: (R)-3-hydroxyacyl-CoA growing poly(3-hydroxyalkanoate) chain
Products: elongated poly(3-hydroxyalkanoate) chain CoA

Processes

poly(3-hydroxyalkanoate) biosynthetic processGO:0042621

Polymerizes medium-chain-length 3-hydroxyacyl monomers into intracellular storage polyester at the PHA granule surface.

Part 3: intracellular PHA mobilization
Intracellular PhaZ depolymerizationReactionmcl_pha_depolymerization

Annotons

Intracellular mcl-PHA depolymerase
intracellular_phaz_depolymerase
Participant: Family: intracellular PhaZ depolymerase family
Family:
intracellular PhaZ depolymerase familyInterPro:IPR011942
Representative Members: PSEPK PhaZUniProtKB:Q88D24 Ectopseudomonas oleovorans PhaZUniProtKB:P26495
Required Function:
closest existing mcl-PHA depolymerase activityGO:0050527

Function

closest existing mcl-PHA depolymerase activityGO:0050527
Substrates: intracellular medium-chain-length poly(3-hydroxyalkanoate) water
Products: medium-chain-length 3-hydroxyalkanoate oligomers and monomers

Processes

poly(3-hydroxyalkanoate) metabolic processGO:0042620

Mobilizes stored mcl-PHA carbon through hydrolysis at the intracellular granule. GO:0050527 is octanoate-specific and is used as the closest existing term; the characterized enzyme accepts broader mcl-PHA polymers.