Bacterial naringenin A-ring degradation

A species-neutral model of the bacterial fde pathway that converts naringenin through hydroxylation and oxygenolytic A-ring cleavage to smaller aromatic products. The module exposes six reaction parts corresponding to KEGG R13074-R13079. FdeE and FdeC have experimental genetic and metabolite support in Herbaspirillum seropedicae, whereas the roles assigned to FdeD, FdeH, FdeJ, FdeB, and FdeI remain pathway and orthology predictions. The module therefore distinguishes required pathway roles from directly established molecular functions and does not treat every co-assigned protein as an independently characterized catalyst.

MODULE:bacterial_flavonoid_degradationDRAFTMetabolic Pathwaymodules/bacterial_flavonoid_degradation.yaml
flavonoid metabolic processGO:0009812
PMID:27059806
Genetic and functional characterization of a novel meta-pathway for degradation of naringenin in Herbaspirillum seropedicae SmR1
Mutant and LC-MS/MS evidence establishes FdeE-dependent naringenin monooxygenation and FdeC-dependent A-ring dioxygenation in H. seropedicae.
KEGG:map00946
Degradation of flavonoids
KEGG supplies the R13074-R13079 reaction chain and K26179-K26185 Fde role assignments; the individual reaction records mark the chemistry as unclear.
file:PSEPK/PP_3197/PP_3197-ai-review.yaml
Pseudomonas putida PP_3197 FdeC-like gene review
The review grounds the FdeC leaf to Q88I05, GO:0016702, and orthology to the experimentally tested Hsero_1005 protein.
file:PSEPK/PP_3199/PP_3199-ai-review.yaml
Pseudomonas putida PP_3199 FdeE-like gene review
The review grounds the FdeE leaf to Q88I03 and a conservative monooxygenase molecular-function term.
file:PSEPK/PP_3195/PP_3195-ai-review.yaml
Pseudomonas putida PP_3195 FdeB-like gene review
The review grounds the predicted FdeB ester-hydrolase role to Q88I07.
file:PSEPK/PP_3206/PP_3206-ai-review.yaml
Pseudomonas putida PP_3206 FdeJ-like gene review
The review supports Q88HZ6 as an FdeJ-like pathway component while leaving its molecular function and the proposed R13076 chemistry unresolved.
file:PSEPK/PP_3204/PP_3204-ai-review.yaml
Pseudomonas putida PP_3204 FdeH-like gene review
The review supports FdeH pathway participation but leaves its molecular function unresolved.
file:PSEPK/PP_3205/PP_3205-ai-review.yaml
Pseudomonas putida PP_3205 FdeI-like gene review
The review supports a predicted FdeI carboxy-lyase role while retaining uncertainty about R13079.
7Nodes
6Parts
0Variant Sets
0Variants
8Annotons
5Connections

Derived QC

Recommended-field compliance

71.4% recommended fields populated
  • module.knowledge_gaps[0] · boundary (0/1)
  • module.knowledge_gaps[0].provenance[0] · reference_section_type (0/1)

Module deep research

✗ none found

No MODULE:bacterial_flavonoid_degradation 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.

Reaction chaining (advisory)

✓ every PRECEDES step chains, or its break is acknowledged via chaining_status.

  • r13074_naringenin_hydroxylation → r13075_a_ring_cleavage [NOT_CHECKED]
    The R13074 product is the R13075 substrate in KEGG map00946.
  • r13075_a_ring_cleavage → r13076_c_c_hydrolysis [NOT_CHECKED]
    The R13075 product C22569 is the R13076 substrate.
  • r13076_c_c_hydrolysis → r13077_lactone_hydrolysis [NOT_CHECKED]
    R13076 produces the delta-lactone consumed by R13077.
  • r13077_lactone_hydrolysis → r13078_decarboxylation [NOT_CHECKED]
    R13077 produces the beta-keto acid consumed by R13078.
  • r13078_decarboxylation → r13079_dehydration [NOT_CHECKED]
    R13078 produces the hydroxyketone consumed by R13079.

Gene-review completeness (7/14 grounded genes reviewed)

7 complete review(s) · 6 with deep research · 7 missing review · 1 reviewed but lacking deep research

Gene Review Complete Deep research
Hsero_1004/FdeB-like protein D8J0W6 ✗ — —
Hsero_1005/FdeC D8J0W7 ✗ — —
Hsero_1006/FdeD-like protein D8J0W8 ✗ — —
Hsero_1007/FdeE D8J0W9 ✗ — —
Hsero_1010/FdeH-like protein D8J0X2 ✗ — —
Hsero_1011/FdeI-like protein D8J0X3 ✗ — —
Hsero_1012/FdeJ-like protein D8J0X4 ✗ — —
PP_3195 Q88I07 ✓ ✓ ✓
PP_3197 Q88I05 ✓ ✓ ✓
PP_3198 Q88I04 ✓ ✓ ✗
PP_3199 Q88I03 ✓ ✓ ✓
PP_3204 Q88HZ8 ✓ ✓ ✓
PP_3205 Q88HZ7 ✓ ✓ ✓
PP_3206 Q88HZ6 ✓ ✓ ✓

Details

Context
bacteriaNCBITaxon:2
bacterial naringenin A-ring degradationMetabolic Pathwaybacterial_flavonoid_degradation
flavonoid metabolic processGO:0009812
Context
bacteriaNCBITaxon:2

Connections

Part 1: naringenin hydroxylation
naringenin to 5,7,8-trihydroxyflavanoneReactionr13074_naringenin_hydroxylation

Annotons

FdeE flavonoid monooxygenase
fdee_monooxygenase
Participant: Family: FdeE naringenin monooxygenase family
Family:
FdeE naringenin monooxygenase family
Representative Members: Hsero_1007/FdeEUniProtKB:D8J0W9 PP_3199 FdeE-like proteinUniProtKB:Q88I03

Function

flavonoid 8-monooxygenase activityGO:0016709
Substrates: naringenin dioxygen
Products: 5,7,8-trihydroxy-2-(4-hydroxyphenyl)-2,3-dihydro-4H-chromen-4-one

FdeE performs the experimentally supported entry monooxygenation. The broad GO term is used because no substrate-specific GO term exists.

FdeD Rieske electron-transfer component
fded_rieske_partner
Participant: Family: FdeD Rieske [2Fe-2S] protein family
Family:
FdeD Rieske [2Fe-2S] protein family
Representative Members: Hsero_1006/FdeD-like proteinUniProtKB:D8J0W8 PP_3198 FdeD-like proteinUniProtKB:Q88I04

Function

2 iron, 2 sulfur cluster bindingGO:0051537

FdeD is associated with R13074 by KEGG, but its electron donor and acceptor have not been established; no direct FdeD-FdeE transfer is asserted.

Part 2: oxygenolytic A-ring cleavage
trihydroxyflavanone dioxygenation and A-ring cleavageReactionr13075_a_ring_cleavage

Annotons

FdeC A-ring-cleaving dioxygenase
fdec_dioxygenase
Participant: Family: FdeC flavonoid A-ring dioxygenase family
Family:
FdeC flavonoid A-ring dioxygenase family
Representative Members: Hsero_1005/FdeCUniProtKB:D8J0W7 PP_3197 FdeC-like proteinUniProtKB:Q88I05

Function

flavonoid A-ring extradiol dioxygenase activityGO:0016702
Substrates: 5,7,8-trihydroxyflavanone dioxygen
Products: A-ring meta-cleavage product C22569

FdeC is the experimentally supported ring-cleavage catalyst; substrate- specific chemistry in species other than H. seropedicae remains inferred.

FdeH cupin component
fdeh_cupin_component
Participant: Family: FdeH cupin-family pathway component
Family:
FdeH cupin-family pathway component
Representative Members: Hsero_1010/FdeH-like proteinUniProtKB:D8J0X2 PP_3204 FdeH-like proteinUniProtKB:Q88HZ8

KEGG co-assigns FdeH to R13075, but available evidence does not show whether it is catalytic, metal-binding, structural, or dispensable.

Part 3: cleavage-product hydrolysis
C22569 to flavonoid-derived delta-lactone and oxaloacetateReactionr13076_c_c_hydrolysis

Annotons

FdeJ pathway component
fdej_c_c_hydrolase
Participant: Family: FdeJ flavonoid-cleavage-product hydrolase family
Family:
FdeJ flavonoid-cleavage-product hydrolase family
Representative Members: Hsero_1012/FdeJ-like proteinUniProtKB:D8J0X4 PP_3206 FdeJ-like proteinUniProtKB:Q88HZ6

KEGG assigns FdeJ to the oxaloacetate-releasing R13076 step, but no FdeJ-family protein has been characterized for this reaction and the epimerase/dehydratase fold does not establish carbon-carbon hydrolase chemistry. No molecular-function term is asserted.

Part 4: delta-lactone ring opening
flavonoid-derived delta-lactone hydrolysisReactionr13077_lactone_hydrolysis

Annotons

FdeB lactone hydrolase
fdeb_ester_hydrolase
Participant: Family: FdeB flavonoid-derived lactone hydrolase family
Family:
FdeB flavonoid-derived lactone hydrolase family
Representative Members: Hsero_1004/FdeB-like proteinUniProtKB:D8J0W6 PP_3195 FdeB-like proteinUniProtKB:Q88I07

Function

flavonoid-derived delta-lactone hydrolase activityGO:0052689
Substrates: 5-(4-hydroxyphenyl)-3-oxovalero-delta-lactone water
Products: 5-hydroxy-5-(4-hydroxyphenyl)-3-oxopentanoate

The exact R13077 lactone substrate remains untested for FdeB-family proteins.

Part 5: beta-keto acid decarboxylation
flavonoid-derived beta-keto acid decarboxylationReactionr13078_decarboxylation

Annotons

FdeI predicted carboxy-lyase
fdei_decarboxylase
Participant: Family: FdeI late flavonoid-degradation enzyme family
Family:
FdeI late flavonoid-degradation enzyme family
Representative Members: Hsero_1011/FdeI-like proteinUniProtKB:D8J0X3 PP_3205 FdeI-like proteinUniProtKB:Q88HZ7

Function

flavonoid-derived beta-keto acid decarboxylase activityGO:0016831
Substrates: 5-hydroxy-5-(4-hydroxyphenyl)-3-oxopentanoate
Products: 4-hydroxy-4-(4-hydroxyphenyl)-butan-2-one carbon dioxide

No direct FdeI-family assay has established R13078.

Part 6: water elimination
hydroxyketone to 4-hydroxycinnamoylmethaneReactionr13079_dehydration

Annotons

unresolved FdeI-associated dehydration
fdei_dehydration_role
Participant: Family: FdeI late flavonoid-degradation enzyme family
Family:
FdeI late flavonoid-degradation enzyme family
Representative Members: Hsero_1011/FdeI-like proteinUniProtKB:D8J0X3 PP_3205 FdeI-like proteinUniProtKB:Q88HZ7

KEGG assigns R13079 to FdeI, but available evidence does not establish whether PP_3205 catalyzes water elimination or whether this conversion is spontaneous or performed by another factor. No MF term is asserted.