Biosynthetic Gene Cluster (BGC) Enzyme Complexes Project

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Biosynthetic Gene Cluster (BGC) Enzyme Complexes Project

Project type: Gene curation (exemplar enzymes from microbial natural-product gene clusters)
Status: Seeding — exemplar genes selected, curation queued

Overview

Biosynthetic gene clusters (BGCs) are contiguous genomic regions encoding the
enzymes that assemble microbial secondary metabolites — antibiotics, siderophores,
quorum-sensing signals, pigments, and mycotoxins. They are attractive targets for
AI-assisted GO curation because:

  1. Function follows pathway context. A protein's molecular function and the
    biological process it contributes to are strongly constrained by the cluster it
    sits in and the compound that cluster makes. This gives an unusually strong
    prior for evaluating (and challenging) existing annotations.
  2. Many cluster members are under- or mis-annotated. Tailoring enzymes,
    carrier proteins, and "uncharacterized" cluster proteins frequently carry only
    generic IEA terms despite well-resolved biochemistry.
  3. Complexes matter. Intermediate channeling, enzymatic regulation, and
    structural stability in BGCs are often mediated by heteromeric enzyme
    complexes that are only functional when assembled     — a fact that is poorly
    reflected in current Cellular Component / "protein-containing complex"
    annotations.

Motivating resource

Moriwaki et al., "High-throughput prediction of protein–protein interactions
uncovers hidden molecular networks in biosynthetic gene clusters" (bioRxiv
10.1101/2025.10.26.684697, v2 2026;
data at Zenodo 10.5281/zenodo.17451667).

The authors replaced AlphaFold3's MSA step with MMseqs2 to run a genome-scale,
all-vs-all complex screen over 2,437 active MIBiG v4.0 BGCs (487,828 protein
pairs), predicting 15,438 heteromeric interactions at ipTM ≥ 0.6, of which
1,390 also showed structural homology (RMSD ≤ 2.0 Å) to known structures.
A curated subset of 381 high-confidence structurally-homologous pairs across 239
BGCs is released, alongside a validation set of ~30 experimentally-solved
heterocomplexes (each tied to a PDB entry) used as positive controls.

This resource is used here as one line of structural evidence (predicted
complex membership / interaction) when reviewing BGC enzyme annotations — analogous
to how projects/ALPHAFOLD.md and projects/PROTEIN_COMPLEX_FUNCTIONS.md use
predicted quaternary structure. Predictions are hypotheses, not facts (see
Caveats).

Exemplar selection criteria

Exemplars are drawn primarily from the paper's PDB-backed validation set (so the
predicted complex corresponds to a real, solved structure), favouring:

All BGC accessions, GenBank protein IDs, PDB IDs, and ipTM/ipSAE values below are
taken directly from the authors' deposited data (verified, not inferred). UniProt
accessions and final gene symbols are resolved at the fetch-gene step.

Candidate exemplar complexes

BGC (MIBiG) Organism (species code) Product Class Protein pair (GenBank) PDB ipTM Notes / annotation angle
BGC0000922 Pseudomonas aeruginosa PAO1 (PSEAE) 2-alkyl-4-quinolones (PQS precursors) PKS aag04386.1 / aag04387.1 5DWZ 0.95 PqsB / PqsC condensing heterodimer of the pqs quorum-sensing pathway; clinically important; classic obligate heterocomplex.
BGC0000194 Streptomyces coelicolor A3(2) (STRCO) actinorhodin type II PKS cac44200.1 / cac44201.1 1TQY 0.96 Model type II PKS tailoring step (ActVA region monooxygenase/cyclase); textbook system.
BGC0000055 Saccharopolyspora erythraea NRRL 2338 (SACEN) erythromycin A–D modular PKS cam00066.1 / cam00067.1 2YJN 0.92 DEBS-associated pair (Hetero 4-mer); modular PKS docking/tailoring; flagship polyketide.
BGC0000610 Streptomyces actuosus (STRAT) nosiheptide RiPP (thiopeptide) acr48346.1 / acr48347.1 8K60 0.88 RiPP maturation enzymes; tests CC/MF annotation of post-translational tailoring complex.
BGC0000127 Pseudomonas protegens Pf-5 (PSEF5) pyoluteorin PKS aad24885.1 / aad24881.1 6O6E 0.76 Lower-confidence positive control — useful "edge case" for calibrating how much weight to give an ipTM≈0.76 prediction.

Stretch / discovery targets (high-confidence novel predictions, not in the
validation set — candidates for -predictions-review.yaml rather than direct
acceptance): BGC0001288 (maklamicin, Micromonospora sp. GMKU326, ipTM 0.95),
BGC0001665 (alkyl-resorcinol, Mycobacterium marinum M, ipTM 0.95).

Curation workflow (per exemplar)

For each protein in a selected complex:

  1. just fetch-gene <SPECIES_CODE> <GENE> — resolve the GenBank accession to its
    UniProt entry and HGNC-style/standard gene symbol, and create the review stub,
    uniprot, and goa files. Record the GenBank→UniProt mapping in
    <GENE>-notes.md     (do not guess identifiers).
  2. Deep-research the gene/pathway; capture provenance inline
    ([PMID:xxxxx "supporting text"]) in <GENE>-notes.md.
  3. Review existing GOA annotations per the standard guidelines (ACCEPT /
    KEEP_AS_NON_CORE / MODIFY / MARK_AS_OVER_ANNOTATED / REMOVE / UNDECIDED). Do
    not REMOVE experimental annotations on the basis of cached abstracts alone.
  4. Use the predicted complex as supporting structural evidence, especially for:
  5. Cellular Component / protein-containing complex membership;
  6. Molecular Function where the activity is only realized in the assembled
    heterocomplex (note this explicitly in core_functions).
    Cite as file:<SPECIES>/<GENE>/... or reference the bioRxiv DOI + PDB ID.
  7. For novel (non-validation) predictions, record adjudication in
    <GENE>-predictions-review.yaml (COR / CNN / LSP / UNC / PLI / NPI / REP).
  8. just validate <SPECIES_CODE> <GENE>.

Status

Gene / protein Complex Stage
PqsB (PSEAE, Q9I4X2) PqsBC condensing heterodimer (non-catalytic subunit) Review complete
PqsC (PSEAE, Q9I4X1) PqsBC condensing heterodimer (catalytic subunit) Review complete
actI-ORF1 / KSα (STRCO, Q02059) actinorhodin KS-CLF (catalytic ketosynthase) Review complete
actI-ORF2 / KSβ-CLF (STRCO, Q02062) actinorhodin KS-CLF (non-catalytic chain-length factor) Review complete
eryCII (SACEN, A4F7P2) EryCII-EryCIII (P450-homologue GT activator; pseudoenzyme) Review complete
eryCIII (SACEN, A4F7P3) EryCII-EryCIII (desosaminyl glycosyltransferase) Review complete
ActVA region pair (STRCO) actinorhodin tailoring Queued
Erythromycin DEBS pair (SACEN) modular PKS Queued
Nosiheptide pair (STRAT) thiopeptide RiPP Queued
Pyoluteorin pair (PSEF5) edge-case control Queued

First worked example: PqsBC (BGC0000922)

The PqsB/PqsC pair validates the project premise. Reviewing both subunits
(PqsB, PqsC) surfaced exactly the annotation issues the
"only-functional-when-assembled" framing predicts:

The predicted complex (ipTM 0.95, matching PDB 5DWZ) agreed with the experimentally
established obligate heterodimer — a positive-control case where the structural
prediction corroborated, rather than drove, the curation.

Second worked example: actinorhodin KS-CLF (BGC0000194)

The S. coelicolor actinorhodin minimal-PKS KSα/KSβ pair (actI-ORF1,
actI-ORF2; predicted at ipTM 0.96, matching PDB 1TQY) is the same
catalytic + non-catalytic heterodimer pattern as PqsBC, and reproduces the same
annotation failure mode from a different protein family:

Emerging pattern for the project: type II PKS / FabH-like condensing systems are
systematically over-annotated with fatty-acid MF/BP terms and mis-assign the complex's
catalytic activity to the non-catalytic subunit. This is a reusable curation signature
for the remaining BGC exemplars.

Third worked example: erythromycin EryCII-EryCIII (BGC0000055)

The S. erythraea desosaminylation pair (eryCII, eryCIII;
predicted ipTM 0.92, matching PDB 2YJN) generalises the pattern beyond
catalytic/non-catalytic condensing enzymes to a catalytic enzyme + pseudoenzyme
activator pair:

The full erythromycin cluster (23 MIBiG genes) is captured as a representative-species
pathway concept in terms/erythromycin_biosynthesis/erythromycin_biosynthesis-notes.md
(S. erythraea; aligned to MIBiG BGC0000055, all genes mapped to UniProt). Only the
desosaminylation node (eryCIII + eryCII) is fully reviewed so far; the concept doc also records
two MIBiG/UniProt annotation discrepancies flagged for upstream correction (eryCII
"3,4-isomerase" → activator pseudoenzyme; eryCI "sensory transduction protein" → transaminase).

This adds a second over-annotation signature to the project: sequence-similarity to a
catalytic family (here cytochrome P450) propagates a full catalytic/cofactor annotation
set onto a pseudoenzyme that has demonstrably lost the active site — flagged whenever
UniProt carries a "lacks the ... binding sites" CAUTION.

Caveats when using the predictions as evidence

References