identifier: traitmech:000114 label: lignin degradation definition: A biopolymer-degradation metabolism in which an organism breaks down lignin, the recalcitrant aromatic heteropolymer of plant cell walls, using oxidative enzymes such as peroxidases and laccases. definition_source: DOI:10.1039/c1np00042j trait_category: METABOLISM term_kind: CLASS mapping_status: REVIEWED parent_traits: - traitmech:000110 synonyms: - synonym_text: ligninolytic synonym_type: RELATED_SYNONYM source: DOI:10.1039/c1np00042j evidence: - reference: DOI:10.1039/c1np00042j notes: Bugg et al. review pathways for degradation of lignin in bacteria and fungi. - reference: DOI:10.1016/j.cbpa.2015.10.018 notes: Cragg et al. cover lignin breakdown as part of lignocellulose degradation across the tree of life. canonical_examples: - taxon_id: NCBITaxon:132919 taxon_label: Rhodococcus jostii note: "bacterial lignin degrader (DypB peroxidase)" reference: PMID:21534568 - taxon_id: NCBITaxon:165695 taxon_label: Sphingobium note: "lignin-aromatic catabolism" reference: PMID:22207743 causal_graphs: - graph_id: lignin_degradation_peroxidase_laccase title: Lignin degradation breaks down aromatic plant biopolymers via oxidative enzymes description: Evidence-backed causal sketch linking peroxidases and laccases to oxidative cleavage of recalcitrant lignin aromatic heteropolymer. nodes: - node_id: lignin_degradation_trait label: lignin degradation node_type: TRAIT grounding: traitmech:000114 description: Oxidative breakdown of lignin in plant cell walls. - node_id: oxidative_enzymes label: peroxidases and laccases node_type: GENE_OR_PROTEIN description: Secreted oxidative enzymes acting on the lignin aromatic framework. - node_id: aromatic_monomers label: aromatic monomers / oligomers node_type: CHEMICAL description: Aromatic compounds released from depolymerized lignin. - node_id: laccase label: laccase node_type: GENE_OR_PROTEIN description: Multi-copper oxidase (EC 1.10.3.2) acting on lignin and using mediators. grounding: UniProtKB:A0A072TFX8 - node_id: dyp_peroxidase label: DyP-type peroxidase node_type: GENE_OR_PROTEIN description: Dye-decolorizing peroxidase (EC 1.11.1.19) contributing to lignin depolymerization. grounding: UniProtKB:A0A024E2S9 - node_id: manganese_peroxidase label: manganese peroxidase node_type: GENE_OR_PROTEIN description: Manganese peroxidase (EC 1.11.1.13) oxidizing Mn2+ to Mn3+. - node_id: lignin_peroxidase label: lignin peroxidase node_type: GENE_OR_PROTEIN description: Lignin peroxidase (EC 1.11.1.14) cleaving lignin interunit bonds. grounding: UniProtKB:A0A0H3L9R0 - node_id: lignin_depolymerization label: lignin depolymerization node_type: BIOLOGICAL_PROCESS description: Extracellular oxidative depolymerization of the lignin polymer. - node_id: mn2_ion label: Mn2+ node_type: CHEMICAL description: Manganous ion, substrate of manganese peroxidase. grounding: CHEBI:29035 - node_id: mn3_oxidant label: Mn3+ diffusible oxidant node_type: CHEMICAL description: Mn3+ generated by MnP that diffuses into lignin acting as oxidant/mediator. - node_id: small_molecule_mediators label: small-molecule mediators node_type: CHEMICAL description: Low-molecular-weight redox mediators extending laccase oxidative reach. - node_id: beta_o4_bond label: beta-O-4 aryl ether bond node_type: CHEMICAL description: Predominant beta-O-4 aryl-ether interunit linkage of lignin. - node_id: ca_cb_bond label: Calpha-Cbeta bond node_type: CHEMICAL description: Calpha-Cbeta carbon-carbon bond in lignin beta-O-4 units. edges: - subject: oxidative_enzymes predicate: enables object: lignin_degradation_trait description: Peroxidases and laccases drive oxidative lignin breakdown. evidence: - reference: DOI:10.1039/c1np00042j notes: Bugg et al. review pathways for degradation of lignin in bacteria and fungi. predicate_id: RO:0002327 - subject: lignin_degradation_trait predicate: produces object: aromatic_monomers description: Lignin oxidation releases aromatic monomers/oligomers. evidence: - reference: DOI:10.1016/j.cbpa.2015.10.018 notes: Cragg et al. cover lignin breakdown as part of lignocellulose degradation. predicate_id: METPO:2000202 - subject: laccase predicate: participates in object: lignin_depolymerization description: Laccase participates in extracellular lignin depolymerization. evidence: - reference: DOI:10.1186/s13068-024-02470-z notes: LME including laccase (EC 1.10.3.2) participated in depolymerization of large lignin polymers; broad across taxa. predicate_id: biolink:participates_in - subject: dyp_peroxidase predicate: participates in object: lignin_depolymerization description: DyP-type peroxidase participates in lignin depolymerization. evidence: - reference: DOI:10.1186/s13068-024-02470-z notes: DyP-decolorizing peroxidase (EC 1.11.1.19) participated in depolymerization of large lignin polymers. predicate_id: biolink:participates_in - subject: manganese_peroxidase predicate: oxidizes object: mn2_ion description: Manganese peroxidase oxidizes Mn2+ to Mn3+ (canonical MnP mechanism). evidence: - reference: DOI:10.3390/polym16172388 notes: Manganese peroxidase oxidizes Mn2+ to Mn3+ (Pei et al. 2024). predicate_id: METPO:2000016 - subject: mn3_oxidant predicate: acts as oxidant for object: lignin_depolymerization description: Mn3+ diffuses into lignin acting as a diffusible oxidant/mediator driving depolymerization. evidence: - reference: DOI:10.1039/d3cc05298b notes: Mn3+ oxidation product diffuses into lignin structure, acting as a diffusible oxidant or mediator (Bugg 2024). - subject: laccase predicate: uses object: small_molecule_mediators description: Laccases can utilise small-molecule mediators to extend oxidative reach. evidence: - reference: DOI:10.1039/d3cc05298b notes: Laccases or multi-copper oxidases can also utilise small molecule mediators (Bugg 2024). - subject: manganese_peroxidase predicate: cleaves object: beta_o4_bond description: MnP cleaves the beta-O-4 bond in phenolic and non-phenolic lignin model dimers. evidence: - reference: DOI:10.1186/s13068-024-02583-5 notes: MnPs could cleave the beta-O-4 bond in phenolic and non-phenolic lignin model dimers (Zhou 2024). - subject: lignin_peroxidase predicate: cleaves object: ca_cb_bond description: Lignin peroxidase cleaves the Calpha-Cbeta bond of beta-O-4 model compounds. evidence: - reference: DOI:10.1186/s13068-023-02447-4 notes: ALiP-P3 breaks the Calpha-Cbeta bond of the beta-O-4 model compound (Gu 2024). curation_history: - timestamp: '2026-06-08T00:00:00Z' curator: claude action: PROPOSED_FROM_RESEARCH changes: Proposed candidate METABOLISM trait (lignin degradation); sub-variant of biopolymer degradation. llm_assisted: true - timestamp: '2026-06-10T14:00:00Z' curator: claude action: CURATED_CAUSAL_GRAPH changes: Added evidence-backed causal graph (oxidative lignin degradation) with RO/METPO predicate groundings; promoted PROPOSED to REVIEWED. llm_assisted: true - timestamp: '2026-06-23T00:00:00Z' curator: claude action: ENRICH_CAUSAL_GRAPH changes: Added 7 evidence-backed generic edges (10 new nodes) from the deep-research report. llm_assisted: true - timestamp: '2026-06-24T17:21:12Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:participates_in×2, METPO:2000016×1). llm_assisted: true - timestamp: '2026-06-24T17:23:32Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:29035×1). llm_assisted: true - timestamp: '2026-06-26T07:15:18Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A072TFX8×1, UniProtKB:A0A024E2S9×1, UniProtKB:A0A0H3L9R0×1). llm_assisted: true