Yeast metabolic engineering

A scoped plan to review GO annotations for 10 central-carbon genes that strain engineers target

AI Gene Review · projects/YEAST_METABOLIC_ENGINEERING · scoping

Bottom line

  • Scoped, not yet started: 10 S. cerevisiae genes chosen, 0 reviewed.
  • The set covers ethanol production (PDC1, ADH1, ADH2), the glycerol byproduct (GPD1, GPD2), glycolysis (HXK1, PFK1, TDH1), anaplerosis (PYC1) and NADPH supply (ZWF1).
  • Goal: check the annotations are accurate enough to support pathway design.

Where the genes sit

Why these genes

  • Engineers raise ethanol or chemical yield by pushing flux to pyruvate and beyond, and by cutting glycerol, which yeast makes to reoxidise surplus NADH.
  • Each step has paralogs (ADH1/ADH2, GPD1/GPD2, HXK1/HXK2, TDH1–3), so GO has to say which isoform does what.
  • Well-characterised enzymes make a good test of whether annotations reach the right specific reaction terms.

Status

Next steps

  • just fetch-gene yeast <GENE> for each of the 10, then deep research and annotation review.
  • Check the list: on glucose, HXK2 is the main hexokinase and TDH3 the main GAPDH; consider reviewing paralog pairs together.
  • Consider a yeast fermentation module (glucose to ethanol plus the glycerol branch) once the reviews exist.

Read more: projects/YEAST_METABOLIC_ENGINEERING.md