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lignin degradation

traitmech:000114 · CLASS · REVIEWED

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.

Lignin degradation breaks down aromatic plant biopolymers via oxidative enzymes

Evidence-backed causal sketch linking peroxidases and laccases to oxidative cleavage of recalcitrant lignin aromatic heteropolymer.

Lignin degradation breaks down aromatic plant biopolymers via oxidative enzymes Interactive directed graph showing evidence-backed causal relationships for lignin degradation.

Edge evidence

  • peroxidases and laccases enables lignin degradation RO:0002327

    Peroxidases and laccases drive oxidative lignin breakdown.

    • DOI:10.1039/c1np00042j Bugg et al. review pathways for degradation of lignin in bacteria and fungi.
  • lignin degradation produces aromatic monomers / oligomers METPO:2000202

    Lignin oxidation releases aromatic monomers/oligomers.

    • DOI:10.1016/j.cbpa.2015.10.018 Cragg et al. cover lignin breakdown as part of lignocellulose degradation.
  • laccase participates in lignin depolymerization biolink:participates_in

    Laccase participates in extracellular lignin depolymerization.

    • DOI:10.1186/s13068-024-02470-z LME including laccase (EC 1.10.3.2) participated in depolymerization of large lignin polymers; broad across taxa.
  • DyP-type peroxidase participates in lignin depolymerization biolink:participates_in

    DyP-type peroxidase participates in lignin depolymerization.

    • DOI:10.1186/s13068-024-02470-z DyP-decolorizing peroxidase (EC 1.11.1.19) participated in depolymerization of large lignin polymers.
  • manganese peroxidase oxidizes Mn2+ METPO:2000016

    Manganese peroxidase oxidizes Mn2+ to Mn3+ (canonical MnP mechanism).

    • DOI:10.3390/polym16172388 Manganese peroxidase oxidizes Mn2+ to Mn3+ (Pei et al. 2024).
  • Mn3+ diffusible oxidant acts as oxidant for lignin depolymerization

    Mn3+ diffuses into lignin acting as a diffusible oxidant/mediator driving depolymerization.

    • DOI:10.1039/d3cc05298b Mn3+ oxidation product diffuses into lignin structure, acting as a diffusible oxidant or mediator (Bugg 2024).
  • laccase uses small-molecule mediators

    Laccases can utilise small-molecule mediators to extend oxidative reach.

    • DOI:10.1039/d3cc05298b Laccases or multi-copper oxidases can also utilise small molecule mediators (Bugg 2024).
  • manganese peroxidase cleaves beta-O-4 aryl ether bond

    MnP cleaves the beta-O-4 bond in phenolic and non-phenolic lignin model dimers.

    • DOI:10.1186/s13068-024-02583-5 MnPs could cleave the beta-O-4 bond in phenolic and non-phenolic lignin model dimers (Zhou 2024).
  • lignin peroxidase cleaves Calpha-Cbeta bond

    Lignin peroxidase cleaves the Calpha-Cbeta bond of beta-O-4 model compounds.

    • DOI:10.1186/s13068-023-02447-4 ALiP-P3 breaks the Calpha-Cbeta bond of the beta-O-4 model compound (Gu 2024).

Provenance

Source
METPO (2025-11-25)
Definition source
DOI:10.1039/c1np00042j

Parent traits (1)

Synonyms (1)

  • ligninolytic RELATED_SYNONYM · DOI:10.1039/c1np00042j

kg-microbe context

Matched 1 kg-microbe node via parent_proxy.

  • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

Nearest neighbors in embedding space

Top-8 cosine-similar METPO traits from the 2026-04-25 deepwalk (512-D).

Curation history

  1. · PROPOSED_FROM_RESEARCH · claude

    Proposed candidate METABOLISM trait (lignin degradation); sub-variant of biopolymer degradation.

  2. · CURATED_CAUSAL_GRAPH · claude

    Added evidence-backed causal graph (oxidative lignin degradation) with RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.

  3. · ENRICH_CAUSAL_GRAPH · claude

    Added 7 evidence-backed generic edges (10 new nodes) from the deep-research report.

  4. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:participates_in×2, METPO:2000016×1).

  5. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:29035×1).

  6. · GROUND_CAUSAL_NODES · claude

    Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A072TFX8×1, UniProtKB:A0A024E2S9×1, UniProtKB:A0A0H3L9R0×1).