TraitMech

TraitMech › METABOLISM

biopolymer degradation

traitmech:000110 · CLASS · REVIEWED

A metabolism in which an organism secretes enzymes to depolymerize recalcitrant biopolymers (such as cellulose, hemicellulose, chitin, and lignin) into assimilable units for growth.

Biopolymer degradation depolymerizes recalcitrant biomass extracellularly

Evidence-backed causal sketch linking secreted depolymerizing enzymes to liberation of assimilable units from recalcitrant biopolymers.

Biopolymer degradation depolymerizes recalcitrant biomass extracellularly Interactive directed graph showing evidence-backed causal relationships for biopolymer degradation.

Edge evidence

  • secreted depolymerizing enzymes enables biopolymer degradation RO:0002327

    Secreted enzymes drive extracellular biopolymer breakdown.

    • DOI:10.1016/j.cbpa.2015.10.018 Cragg et al. review the complementary enzymes used to deconstruct plant biopolymers across the tree of life.
  • biopolymer degradation produces assimilable mono- and oligosaccharides METPO:2000202

    Depolymerization releases assimilable units for cellular uptake.

    • DOI:10.1128/MMBR.66.3.506-577.2002 Lynd et al. review microbial cellulose utilization as the archetypal biopolymer-degradation process.
  • endoglucanase cleaves cello-oligosaccharides

    Endoglucanases hydrolyze internal beta-1,4 bonds in cellulose to release cello-oligosaccharides.

    • DOI:10.1101/2024.11.06.622210 Hsin 2024: "Endoglucanases ... cleave internal beta-1,4 linkages" (strong, general).
  • beta-glucosidase converts glucose

    Beta-glucosidases convert cellobiose/oligosaccharides to glucose (terminal saccharification).

    • DOI:10.1101/2024.11.06.622210 Hsin 2024: "beta-glucosidases ... convert cellobiose/oligosaccharides to glucose" (strong, general).
  • SusC-like TonB-dependent transporter imports oligosaccharides METPO:2000208

    SusC-like TonB-dependent transporter imports oligosaccharides across the outer membrane into the periplasm.

    • DOI:10.1128/mbio.02599-23 Wong 2024: "SusC is a TonB-dependent transporter that imports maltooligosaccharides into the periplasm" (strong).
  • periplasmic GH3 hydrolase converts glucose

    Periplasmic GH3 hydrolases depolymerize imported oligomers to glucose after uptake.

    • DOI:10.3389/fmicb.2024.1393588 Kalenborn 2024: "conversion of oligomeric laminarin to glucose in the periplasm can be catalyzed by ... glycosyl hydrolases" (strong).
  • endo-chitinase depolymerizes chitooligosaccharides

    Endo-chitinases cleave internally within chitin to produce chitooligosaccharides.

    • DOI:10.1128/spectrum.00886-24 Meunier 2024: "endo-chitinases EC 3.2.1.14 cleaving internally to produce multimers" (strong).
  • lignin-oxidizing redox enzymes (LiP/MnP/VP/laccase/DyP) depolymerizes lignin

    Secreted oxidative redox enzymes (LiP/MnP/VP/laccase/DyP) depolymerize lignin.

    • DOI:10.1101/2024.11.06.622210 Hsin 2024: "white-rot species deploy multiple oxidative enzymes (DyPs, LCMOs, LiP, MnP, LaC, VP)".

Provenance

Source
METPO (2025-11-25)
Definition source
DOI:10.1016/j.cbpa.2015.10.018

Parent traits (1)

Children (6)

Synonyms (1)

  • biomass degradation RELATED_SYNONYM · DOI:10.1016/j.cbpa.2015.10.018

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 axis class (biopolymer degradation) to parent cellulolysis, chitinolysis, xylan degradation, and lignin degradation.

  2. · CURATED_CAUSAL_GRAPH · claude

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

  3. · ENRICH_CAUSAL_GRAPH · claude

    Added 6 evidence-backed generic edges (11 new nodes) from the deep-research report.

  4. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000208×1).

  5. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:17234×1).

  6. · GROUND_CAUSAL_NODES · claude

    Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:50699×1, CHEBI:6457×1).

  7. · GROUND_CAUSAL_NODES · claude

    Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A060H8L4×1, UniProtKB:A0A031JNC1×1, UniProtKB:Q693B6×1).