Bacillus subtilis

Reviewing GO annotations on 29 genes of the model Gram-positive bacterium

AI Gene Review · projects/BACSU · 2026

Bottom line

  • We reviewed every GO annotation on 29 genes in three rounds: CACAO-curated genes, key functional genes, and the sporulation sigma cascade plus industrial enzymes.
  • 343 rows: 200 accepted, 28 kept as non-core, 45 modified, 44 NEW, 14 removed, 10 over-annotated, 2 undecided.
  • Recurring fixes: sigma factors are not RNA polymerases, a fold-based acyltransferase call on spoVAD removed, rows citing a paper that never mentions the gene removed.

Why B. subtilis

  • Model Gram-positive bacterium, the counterpart to E. coli.
  • Model for cell differentiation: sporulation runs on a cascade of compartment-specific sigma factors.
  • Naturally competent, and an industrial secretion host (subtilisin, amylase, levansucrase).
  • Round 1 targeted genes where CACAO student curation had contributed heavily, to test those rows.

The sporulation sigma cascade

Sigma factors are not polymerases

sigG review: IBA rows for RNA polymerase activity (GO:0003899) and cis-regulatory region binding (GO:0000976) removed; the correct function is GO:0016987 sigma factor activity. Same calls on sigF and sigK.

Results across 29 genes

Notable findings

  1. PMID:25313396 lists the minimal FlgM-secretion components and does not include fliH, fliY or swrD. Rows citing it were removed (fliY, swrD) or left UNDECIDED (fliH).
  2. spoVAD: acyltransferase activity came from a thiolase-like fold; it is a Ca-DPA channel component. Removed.
  3. yddE is labelled uncharacterized in UniProt but is ConE, the VirB4-like ATPase of the ICEBs1 conjugation system.
  4. Generic metal ion binding refined to zinc / calcium binding (nprE); hydrolase activity marked over-annotated where specific terms exist.

Status and next steps

  • ✅ 29/29 reviews present and rendered; sporulation cascade pathway summary written.
  • ⬜ Most YAML files still say status: DRAFT; fliH has 2 UNDECIDED rows.
  • ⬜ Fix the project tables: several UniProt IDs differ from the reviewed accessions (lipA is reviewed as lipoyl synthase O32129).

Read more: projects/BACSU.md · projects/BACSU/BACSU_SPORULATION-pathway.md · genes/BACSU/<gene>/