Ubiquinone biosynthesis from chorismate-derived 4-hydroxybenzoate

Reusable bacterial pathway for de novo aerobic biosynthesis of ubiquinone (coenzyme Q) from chorismate-derived 4-hydroxybenzoate and a supplied polyprenyl diphosphate side chain. UbiC forms the aromatic head group, UbiA attaches the side chain, and UbiD decarboxylates the prenylated intermediate using prenylated FMN supplied by UbiX. Three complementary ring hydroxylations and three methylations then generate mature ubiquinone. The identities of the aerobic hydroxylases vary by lineage; Coq7-family enzymes can replace the UbiF-type late hydroxylase. UbiJ, UbiK, and UbiB are modeled as optional bacterial assembly/ATP-dependent accessory context rather than reaction chemistry. Oxygen-independent UbiT/UbiU/UbiV implementations are a distinct conditional variant and are outside this aerobic module.

MODULE:ubiquinone_biosynthesisDRAFTMetabolic Pathwaymodules/ubiquinone_biosynthesis.yaml
ubiquinone biosynthetic processGO:0006744
GO:0006744
ubiquinone biosynthetic process
GO biological-process term for de novo ubiquinone biosynthesis; used as the primary process grounding for the module.
KEGG:map00130
Ubiquinone and other terpenoid-quinone biosynthesis
KEGG pathway context for ubiquinone biosynthesis and neighboring terpenoid-quinone reactions; species-specific map members need filtering because quinone reductases, homogentisate metabolism, menaquinone methylation, and cofactor-supply enzymes can appear in the same map.
PMID:28927698
Biochemistry of Mitochondrial Coenzyme Q Biosynthesis
Review article summarizing CoQ/ubiquinone biosynthesis across eukaryotic and prokaryotic systems, including the UbiD/UbiX decarboxylation context, prokaryotic UbiG O-methylation, UbiE/COQ5 C-methylation, UbiH-like hydroxylation, and COQ7/Coq7 late hydroxylation.
PMID:24480387
Biosynthesis and physiology of coenzyme Q in bacteria
Review of bacterial ubiquinone reaction order, enzyme assignments, and pathway variation used to delimit the reaction chain.
PMID:23709220
ubiI, a new gene in Escherichia coli coenzyme Q biosynthesis, is involved in aerobic C5-hydroxylation
Establishes UbiI as the oxygen-dependent early polyprenylphenol hydroxylase and grounds the experimentally characterized E. coli exemplar UniProtKB:P25535.
PMID:30686758
A soluble metabolon synthesizes the isoprenoid lipid ubiquinone
Establishes the bacterial Ubi metabolon and the lipid-intermediate handling role of the UbiJ scaffold.
PMID:36142227
Towards Molecular Understanding of the Functional Role of UbiJ-UbiK(2) Complex in Ubiquinone Biosynthesis by Multiscale Molecular Modelling Studies
Supports the bacterial UbiJ/UbiK accessory assembly context while distinguishing it from the core reaction sequence.
file:modules/ubiquinone_biosynthesis-deep-research-openscientist.md
OpenScientist generic ubiquinone module review
Research synthesis covering module boundaries, reaction order, oxygen-dependent alternatives, and bacterial assembly factors.
file:projects/P_PUTIDA/deep-research/PSEPK__ubiquinone_biosynthesis__ppu00130-deep-research-openscientist.md
OpenScientist PSEPK ubiquinone pathway assessment
Species-level satisfiability audit identifying the complete KT2440 aerobic route, the Coq7-for-UbiF substitution, and UbiJ/UbiK/UbiB accessory factors omitted by KEGG map membership.
file:projects/P_PUTIDA/data/psepk_gene_list.tsv
PSEPK UniProt metadata inventory
Local UniProt-derived inventory provides the Pseudomonas putida KT2440 exemplar accessions, GO terms, EC numbers, and PANTHER families used to ground representative members in this module.

This module is intentionally narrower than KEGG map00130: it represents aerobic ubiquinone biosynthesis, not all terpenoid quinones. Homogentisate production, generic NAD(P)H:quinone oxidoreductases, acyl-CoA thioesterases, menaquinone synthesis, and downstream quinone use are outside the boundary. Polyprenyl diphosphate synthesis is an upstream isoprenoid-module input, so IspB/PDSS enzymes are not duplicated here. Exact ring-tailoring order and substrate names differ among lineages; connections across the grouped hydroxylation and methylation submodules therefore record pathway continuity without claiming one universal order for every intermediate.

7Nodes
6Parts
0Variant Sets
0Variants
13Annotons
7Connections

Derived QC

Recommended-field compliance

53.8% recommended fields populated
  • module.knowledge_gaps[0] · status (0/1)
  • module.knowledge_gaps[0] · provenance (0/1)
  • module.knowledge_gaps[1] · status (0/1)
  • module.knowledge_gaps[1] · provenance (0/1)
  • module.knowledge_gaps[2] · status (0/1)
  • module.knowledge_gaps[2] · provenance (0/1)

Module deep research

✓ present

  • ubiquinone_biosynthesis-deep-research-openscientist.md (openscientist)

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 (12/24 grounded genes reviewed)

12 complete review(s) · 12 with deep research · 12 missing review · 0 reviewed but lacking deep research

Gene Review Complete Deep research
coq7 Q88QR1 ✓ ✓ ✓
ubiB (Escherichia coli K-12) P0A6A0 ✗ — —
ubiE (Escherichia coli K-12) P0A887 ✗ — —
ubiD (Escherichia coli K-12) P0AAB4 ✗ — —
ubiJ (Escherichia coli K-12) P0ADP7 ✗ — —
ubiX (Escherichia coli K-12) P0AG03 ✗ — —
ubiA (Escherichia coli K-12) P0AGK1 ✗ — —
ubiG (Escherichia coli K-12) P17993 ✗ — —
ubiH (Escherichia coli K-12) P25534 ✗ — —
ubiI (Escherichia coli K-12) P25535 ✗ — —
ubiC (Escherichia coli K-12) P26602 ✗ — —
ubiK (Escherichia coli K-12) Q46868 ✗ — —
coq7 (Pseudomonas aeruginosa PAO1) Q9I5R6 ✗ — —
ubiA Q88C65 ✓ ✓ ✓
ubiB A0A140FWS4 ✓ ✓ ✓
ubiC Q88C66 ✓ ✓ ✓
ubiD Q88CG8 ✓ ✓ ✓
ubiE Q88D17 ✓ ✓ ✓
ubiG Q88M10 ✓ ✓ ✓
ubiH Q88CI2 ✓ ✓ ✓
ubiJ Q88D16 ✓ ✓ ✓
ubiK Q88CE6 ✓ ✓ ✓
ubiX Q88QE6 ✓ ✓ ✓
visC Q88CI4 ✓ ✓ ✓

Details

Ubiquinone biosynthesisMetabolic Pathwayubiquinone_biosynthesis
ubiquinone biosynthetic processGO:0006744

Connections

Part 1: aromatic head-group synthesis
4-hydroxybenzoate formation from chorismateReactionhydroxybenzoate_head_group_synthesis

Annotons

UbiC: chorismate lyase
chorismate_lyase_activity
Participant: Family: UbiC chorismate lyase family
Family:
UbiC chorismate lyase familyPANTHER:PTHR38683
Representative Members: ubiC (Pseudomonas putida KT2440)UniProtKB:Q88C66 ubiC (Escherichia coli K-12)UniProtKB:P26602

Function

chorismate lyase activityGO:0008813
Substrates: chorismate
Products: 4-hydroxybenzoate pyruvate

Supplies the aromatic head group precursor for ubiquinone.

Part 2: polyprenyl side-chain attachment
Polyprenylation of 4-hydroxybenzoateReactionhydroxybenzoate_prenylation

Annotons

UbiA: 4-hydroxybenzoate polyprenyltransferase
hydroxybenzoate_polyprenyltransferase_activity
Participant: Family: UbiA 4-hydroxybenzoate polyprenyltransferase family
Family:
UbiA 4-hydroxybenzoate polyprenyltransferase familyPANTHER:PTHR11048
Representative Members: ubiA (Pseudomonas putida KT2440)UniProtKB:Q88C65 ubiA (Escherichia coli K-12)UniProtKB:P0AGK1

Function

4-hydroxybenzoate polyprenyltransferase activityGO:0008412
Substrates: 4-hydroxybenzoate polyprenyl diphosphate
Products: 3-polyprenyl-4-hydroxybenzoate diphosphate

Locations

plasma membraneGO:0005886

Attaches the hydrophobic polyprenyl side chain to the aromatic head group.

Part 3: UbiD decarboxylation and prFMN cofactor supply
prFMN-dependent decarboxylationMetabolic Pathwayubid_decarboxylation_module

UbiD-family decarboxylases require a prenylated-FMN cofactor made by UbiX. UbiX is modeled here as cofactor-supply context for the UbiD step rather than as a direct ring-substrate conversion.

Annotons

UbiX: flavin prenyltransferase
flavin_prenyltransferase_activity
Participant: Family: UbiX flavin prenyltransferase family
Family:
UbiX flavin prenyltransferase familyPANTHER:PTHR43374
Representative Members: ubiX (Pseudomonas putida KT2440)UniProtKB:Q88QE6 ubiX (Escherichia coli K-12)UniProtKB:P0AG03

Function

flavin prenyltransferase activityGO:0106141
Substrates: reduced FMN (FMNH2) dimethylallyl phosphate
Products: prenylated FMNH2 phosphate

Supplies the prenylated-FMN cofactor needed by UbiD-family decarboxylases.

UbiD: 4-hydroxy-3-polyprenylbenzoate decarboxylase
polyprenyl_hydroxybenzoate_decarboxylase_activity
Participant: Family: UbiD prFMN-dependent decarboxylase family
Family:
UbiD prFMN-dependent decarboxylase familyPANTHER:PTHR30108
Representative Members: ubiD (Pseudomonas putida KT2440)UniProtKB:Q88CG8 ubiD (Escherichia coli K-12)UniProtKB:P0AAB4

Function

4-hydroxy-3-polyprenylbenzoate decarboxylase activityGO:0008694
Substrates: 3-polyprenyl-4-hydroxybenzoate
Products: 2-polyprenylphenol carbon dioxide
Cofactors: prenylated FMN

Decarboxylates the prenylated 4-hydroxybenzoate intermediate.

Part 4: aromatic ring hydroxylation
Hydroxylation of prenylated ubiquinone intermediatesMetabolic Pathwayubiquinone_ring_hydroxylation

Hydroxylation steps tailor the prenylated aromatic ring. Bacterial implementations vary, and candidate names can differ across organisms, so this node records the activity-level roles rather than a single universal gene order.

Annotons

UbiH/VisC-family: 2-polyprenylphenol 6-hydroxylase
polyprenylphenol_hydroxylase_activity
Participant: Family: UbiH/VisC ubiquinone hydroxylase family
Family:
UbiH/VisC ubiquinone hydroxylase familyPANTHER:PTHR43876
Representative Members: visC (Pseudomonas putida KT2440)UniProtKB:Q88CI4 ubiI (Escherichia coli K-12)UniProtKB:P25535

Function

2-polyprenylphenol 6-hydroxylase activityGO:0019168
Substrates: 2-polyprenylphenol NADPH oxygen
Products: 2-polyprenyl-6-hydroxyphenol NADP+ water
Cofactors: FAD

Adds a ring hydroxyl group to an early prenylated aromatic intermediate.

UbiH: 2-octaprenyl-6-methoxyphenol hydroxylase
octaprenyl_methoxyphenol_hydroxylase_activity
Participant: Family: UbiH/VisC ubiquinone hydroxylase family
Family:
UbiH/VisC ubiquinone hydroxylase familyPANTHER:PTHR43876
Representative Members: ubiH (Pseudomonas putida KT2440)UniProtKB:Q88CI2 ubiH (Escherichia coli K-12)UniProtKB:P25534

Function

2-octaprenyl-6-methoxyphenol hydroxylase activityGO:0008681
Substrates: 2-octaprenyl-6-methoxyphenol reduced nicotinamide cofactor oxygen
Products: 2-octaprenyl-6-methoxy-1,4-benzoquinol oxidized nicotinamide cofactor water
Cofactors: FAD

Hydroxylates a methoxy-substituted ubiquinone intermediate.

Coq7: 3-demethoxyubiquinol 3-hydroxylase
demethoxyubiquinol_hydroxylase_activity
Participant: Family: Coq7 demethoxyubiquinol hydroxylase family
Family:
Coq7 demethoxyubiquinol hydroxylase familyPANTHER:PTHR11237
Representative Members: coq7 (Pseudomonas putida KT2440)UniProtKB:Q88QR1 coq7 (Pseudomonas aeruginosa PAO1)UniProtKB:Q9I5R6

Function

3-demethoxyubiquinol 3-hydroxylase activityGO:0008682
Substrates: 3-demethoxyubiquinol reduced electron donor oxygen
Products: 3-demethylubiquinol oxidized electron donor water
Cofactors: diiron center

Locations

plasma membraneGO:0005886

Performs the late C-3 hydroxylation needed before final methylation.

Part 5: aromatic ring methylation
O- and C-methylation of ubiquinone intermediatesMetabolic Pathwayubiquinone_ring_methylation

Annotons

UbiG: 2-polyprenyl-6-hydroxyphenol methylase
early_o_methyltransferase_activity
Participant: Family: UbiG ubiquinone O-methyltransferase family
Family:
UbiG ubiquinone O-methyltransferase familyPANTHER:PTHR43464
Representative Members: ubiG (Pseudomonas putida KT2440)UniProtKB:Q88M10 ubiG (Escherichia coli K-12)UniProtKB:P17993

Function

2-polyprenyl-6-hydroxyphenol methylase activityGO:0102208
Substrates: 2-polyprenyl-6-hydroxyphenol S-adenosyl-L-methionine
Products: 2-polyprenyl-6-methoxyphenol S-adenosyl-L-homocysteine

Performs an O-methylation on an early hydroxylated ubiquinone intermediate.

UbiE: 2-methoxy-6-polyprenyl-1,4-benzoquinol methyltransferase
c_methyltransferase_activity
Participant: Family: UbiE/Coq5 ubiquinone C-methyltransferase family
Family:
UbiE/Coq5 ubiquinone C-methyltransferase familyPANTHER:PTHR43591
Representative Members: ubiE (Pseudomonas putida KT2440)UniProtKB:Q88D17 ubiE (Escherichia coli K-12)UniProtKB:P0A887

Function

2-methoxy-6-polyprenyl-1,4-benzoquinol methyltransferase activityGO:0008425
Substrates: 2-methoxy-6-polyprenyl-1,4-benzoquinol S-adenosyl-L-methionine
Products: 2-methoxy-6-polyprenyl-3-methyl-1,4-benzoquinol S-adenosyl-L-homocysteine

Adds the ring C-methyl group during ubiquinone biosynthesis.

UbiE-family enzymes can also support menaquinone methylation; this annoton represents the ubiquinone-biosynthesis activity.

UbiG: 3-demethylubiquinol 3-O-methyltransferase
late_o_methyltransferase_activity
Participant: Family: UbiG ubiquinone O-methyltransferase family
Family:
UbiG ubiquinone O-methyltransferase familyPANTHER:PTHR43464
Representative Members: ubiG (Pseudomonas putida KT2440)UniProtKB:Q88M10 ubiG (Escherichia coli K-12)UniProtKB:P17993

Function

3-demethylubiquinol 3-O-methyltransferase activityGO:0061542
Substrates: 3-demethylubiquinol S-adenosyl-L-methionine
Products: ubiquinol S-adenosyl-L-homocysteine

Performs the final O-methylation yielding ubiquinol/ubiquinone.

Part 6: bacterial metabolon assembly and ATP-dependent accessory support (optional)
Ubiquinone biosynthesis assembly and accessory factorsModuleubiquinone_biosynthesis_accessory_system

Many bacteria organize hydrophobic ring-tailoring intermediates in a Ubi metabolon. UbiJ provides a lipid-binding scaffold, UbiK associates with UbiJ and supports efficient pathway flux, and UbiB-family proteins provide a kinase-like ATP-dependent pathway activity whose direct molecular output remains unresolved. These factors are optional at the species-neutral boundary because their presence and replacement vary across lineages, and none is modeled as a core ring reaction.

Annotons

UbiJ: lipid-binding metabolon scaffold
ubij_metabolon_scaffold
Participant: Family: UbiJ accessory factor family
Family:
UbiJ accessory factor familyPANTHER:PTHR38693
Representative Members: ubiJ (Pseudomonas putida KT2440)UniProtKB:Q88D16 ubiJ (Escherichia coli K-12)UniProtKB:P0ADP7

Processes

ubiquinone biosynthetic processGO:0006744

Binds and shields hydrophobic polyprenylated intermediates within the soluble bacterial Ubi metabolon.

PMID:30686758
UbiJ supplies the lipid-binding cavity of the soluble Ubi metabolon.
UbiK: metabolon accessory factor
ubik_metabolon_accessory_factor
Participant: Family: UbiK accessory factor family
Family:
UbiK accessory factor familyPANTHER:PTHR38040
Representative Members: ubiK (Pseudomonas putida KT2440)UniProtKB:Q88CE6 ubiK (Escherichia coli K-12)UniProtKB:Q46868

Processes

ubiquinone biosynthetic processGO:0006744

Associates with UbiJ and supports efficient assembly or operation of the bacterial Ubi metabolon.

PMID:36142227
Structural modeling supports a functional UbiJ-UbiK2 assembly.
UbiB: ATP-dependent pathway accessory factor
ubib_pathway_accessory_factor
Participant: Family: bacterial UbiB/ABC1 kinase-like family
Family:
bacterial UbiB/ABC1 kinase-like familyPANTHER:PTHR10566
Representative Members: ubiB (Pseudomonas putida KT2440)UniProtKB:A0A140FWS4 ubiB (Escherichia coli K-12)UniProtKB:P0A6A0

Processes

ubiquinone biosynthetic processGO:0006744

Conserved kinase-like ATP-dependent accessory factor required for bacterial ubiquinone biosynthesis; neither a protein-kinase target nor a direct molecular output is asserted at module level.

PMID:10960098
E. coli ubiB disruption eliminates CoQ and accumulates octaprenylphenol.
file:PSEPK/ubiB/ubiB-deep-research-openscientist.md
The P. putida exemplar has no direct experimental characterization; its pathway and ATP-dependent accessory roles are transferred from conserved UbiB-family evidence.