Plant bioenergy modules

Taxon-neutral modules for cell-wall recalcitrance and seed oil

AI Gene Review · projects/PLANT_BIOENERGY · 2026

Bottom line

  • Biofuel yield depends on cell-wall recalcitrance (lignin, xylan acetylation, cellulose crystallinity) and, for oilseeds, triacylglycerol flux and packaging.
  • We curated three new modules (lignin, xylan, seed TAG; PR #2066) and grouped them with the existing cellulose and photosynthesis modules.
  • All five validate and are DRAFT; together they ground 48 UniProt exemplars. Feedstock-species gene reviews have not started.

The five modules

Why modules first

  • The enzymes are well characterized in Arabidopsis, but the feedstocks are poplar, sorghum, maize, rice, soybean.
  • A taxon-neutral module gives each later ortholog review a shared, verified map of steps and GO terms.
  • Identifiers are grounded only where verified; members are exemplars, not species restrictions.

Module inventory

Module Scope UniProt exemplars Status
Lignin (monolignol) PAL → CAD grid, export, radical coupling 14 DRAFT
Xylan IRX9/10/14 backbone, GUX, GXM, O-acetylation 10 DRAFT
Seed TAG Kennedy pathway, PDAT, oleosins 9 DRAFT
Cellulose CESA rosettes, KORRIGAN, COBRA 9 DRAFT
Photosynthesis light reactions + CBB cycle 6 DRAFT

Distinct UniProtKB ids counted in each modules/*.yaml.

A module page

pages/modules/lignin_monolignol_biosynthesis.html: grounded in GO:0009809 lignin biosynthetic process, with Arabidopsis exemplars such as PAL1 and C4H.

Engineering levers

Use case Module(s) Lever
Lignocellulosic sugars lignin, xylan, cellulose lower lignin, raise S/G, less acetylation, alter crystallinity
Fewer fermentation inhibitors xylan reduce O-acetylation (acetate)
Biodiesel / oleochemicals seed TAG DGAT/PDAT flux, oil-body capacity
Feedstock productivity photosynthesis upstream carbon assimilation

Status and next steps

  • ✅ Five modules curated and validated (all DRAFT).
  • ⬜ Grass-specific modules: mixed-linkage glucan (CSLF/CSLH), arabinoxylan arabinosylation / feruloylation.
  • ⬜ Suberin and cutin biosynthesis.
  • ⬜ Per-gene reviews for poplar / sorghum orthologs of the exemplar enzymes.

Read more: projects/PLANT_BIOENERGY.md · modules/{lignin_monolignol,xylan,seed_triacylglycerol,cellulose}_biosynthesis.yaml