Contested Function Project
Overview
This project tracks genes where GO annotations incorrectly describe the molecular function based on sequence homology or domain presence, but biochemical evidence demonstrates the protein has evolved away from that function. These are compelling cases for AI-assisted curation because they require synthesizing multiple evidence types:
- Sequence/domain homology - suggests one function
- Biochemical assays - demonstrate lack of activity
- Mutational analysis - shows function retained without catalytic activity
- Alternative mechanisms - protein functions through non-enzymatic means
Such genes are often annotated based on IBA (phylogenetic inference) or IEA (electronic annotation) from domains, but these annotations can be misleading when the protein is a pseudo-enzyme or has evolved a divergent function.
Categories of Contested Functions
1. Pseudo-enzymes
Proteins with enzyme-like domains that lack catalytic activity due to:
- Degenerate active site residues
- Loss of cofactor binding
- Structural changes incompatible with catalysis
2. Moonlighting Functions
Proteins where the primary function differs from the one suggested by domain architecture.
3. Over-annotated Binding
Generic "protein binding" or "metal binding" annotations based on domains that don't reflect actual binding specificity or lack of binding.
Featured Examples
Epe1 (S. pombe) - Pseudo-demethylase
The Problem: Epe1 contains a JmjC domain typically associated with histone demethylase activity. Multiple annotations exist for:
- GO:0032452 histone demethylase activity (IBA)
- GO:0032454 histone H3K9 demethylase activity (IDA, EXP)
- GO:0140680 histone H3K36me/H3K36me2 demethylase activity (IEA)
- GO:0051213 dioxygenase activity (IEA)
- GO:0016491 oxidoreductase activity (IEA)
- GO:0046872 metal ion binding (IEA)
The Evidence Against:
1. Epe1 JmjC domain has HVD instead of canonical HXD motif
2. Lacks conserved Fe(II)-binding histidine residues
3. Mass spectrometry assays show NO demethylation of H3K9me2/me3 peptides
4. H297A catalytic mutant retains full anti-silencing function
5. C-terminus alone (without JmjC) disrupts heterochromatin
Actual Function: Non-enzymatic anti-silencing factor that:
- Binds HP1/Swi6 to recruit SAGA histone acetyltransferase complex
- Recruits Bdf2 bromodomain protein to heterochromatin boundaries
- Promotes nucleosome turnover
- Functions as chromatin reader, not eraser
AI Review Action: REMOVE all enzymatic activity annotations; propose replacement with binding terms.
Source: Presented at Gene Ontology Consortium Meeting, October 2025, Cambridge UK. See ai4curation/ai-gene-review.
Genes for Review
Priority 1: Documented Pseudo-enzymes
| Species | Gene | Domain | Contested Function | Status |
|---|---|---|---|---|
| pombe | Epe1 | JmjC | histone demethylase activity | COMPLETE |
Priority 2: Suspected Pseudo-enzymes
(To be identified through literature and bioinformatics)
Priority 3: Over-annotated Domains
(Genes with generic domain-based annotations that require refinement)
Criteria for Inclusion
A gene belongs in this project if:
- Has annotations for enzymatic activity based on domain homology
- Biochemical evidence demonstrates lack of that specific activity
- The protein has an alternative, non-catalytic function
- The case illustrates broader curation principles
Key References
- Raiymbek et al. (2020) - Epe1 biochemical characterization
- Bao et al. (2019) - Epe1 SAGA recruitment mechanism
- Trewick et al. (2007) - Original observation of degenerate JmjC
- Wang et al. (2013) - Epe1/Bdf2 boundary formation
Related Projects
- YEAST_EPIGENETICS_HISTONE_INHERITANCE.md - S. pombe heterochromatin genes
STATUS
Completed Reviews
- [x] pombe/Epe1 - Pseudo-demethylase, chromatin boundary factor
Pending
- [ ] Identify additional pseudo-enzyme candidates
- [ ] Screen for over-annotated IBA/IEA annotations in reviewed genes
Last updated: 2026-01-22
NOTES
2026-01-22
Project Creation
Created project to document genes with contested molecular functions, starting with Epe1 from the GO Consortium 2025 presentation slides.
Epe1 Summary:
- Full review in genes/pombe/[Epe1](../../genes/SCHPO/Epe1/Epe1-ai-review.html)/Epe1-ai-review.yaml
- 5 enzymatic annotations marked REMOVE:
- GO:0032452 histone demethylase activity (IBA)
- GO:0032454 histone H3K9 demethylase activity (IDA x2)
- GO:0140680 histone H3K36me/H3K36me2 demethylase activity (IEA)
- GO:0051213 dioxygenase activity (IEA)
- GO:0016491 oxidoreductase activity (IEA)
- GO:0046872 metal ion binding (IEA)
- Key evidence: Mass spectrometry assays, degenerate active site residues, catalytic mutant retains function
- Proposed replacements: GO:0042393 histone binding, GO:0140030 modification-dependent protein binding
- 6 core functions documented with supporting evidence
This case demonstrates how AI review can integrate:
1. Domain-based predictions (suggests demethylase)
2. Phylogenetic inference (IBA from related proteins)
3. Direct biochemical evidence (no activity)
4. Genetic evidence (mutant analysis)
5. Literature synthesis (alternative mechanism)
The Epe1 review serves as a template for identifying and documenting other pseudo-enzymes.