SGF11
S. cerevisiae
SAGA histone acetyltransferase complex subunit SGF11
What the model saw
Gene: SGF11 Organism: Saccharomyces cerevisiae Known functions: SAGA histone acetyltransferase complex subunit SGF11. enzyme activator activity. protein binding. transcription coactivator activity. zinc ion binding.
View unredacted entry
SAGA histone acetyltransferase complex subunit SGF11. enzyme activator activity. protein binding. transcription coactivator activity. zinc ion binding.
Solver output
SGF11 is a subunit of the SAGA (Spt-Ada-Gcn5-Acetyltransferase) complex, specifically within its deubiquitylase (DUB) module, where it activates the Ubp8 deubiquitylase to remove monoubiquitin from histone H2B. H2B ubiquitination (H2Bub1) is a mark associated with transcriptional elongation and has been linked to chromatin regulation relevant to aging. Loss of H2Bub1 via SGF11/Ubp8 activity alters the epigenetic landscape in ways that can promote gene expression changes detrimental to longevity. In yeast, deletion of SAGA DUB module components, including SGF11, has been associated with extended replicative lifespan, suggesting that SGF11's normal function (promoting H2B deubiquitylation) is anti-longevity. The zinc ion binding activity is consistent with SGF11's structural role in coordinating the DUB module via a zinc finger domain essential for Ubp8 activation. Thus, SGF11's normal enzymatic activator role within SAGA opposes longevity by modulating histone ubiquitination states and downstream transcriptional programs.
GenAge curators classify each gene's normal function as promoting (Pro-Longevity) or opposing (Anti-Longevity) longevity, based on synthesis across studies. Loss-of-function effects can vary from this depending on the manipulation.
Advisor judgment
The model correctly predicted SGF11 as anti_longevity. The mechanistic reasoning is detailed and accurate: SGF11 is indeed part of the SAGA DUB module, activates Ubp8 deubiquitylase, removes monoubiquitin from H2B, and deletion of SGF11 extends replicative lifespan in yeast. The zinc finger domain role is correctly noted. The confidence of 0.65 is reasonable given the specificity of the knowledge required. Overall, this is an excellent prediction with correct answer and correct mechanism.
Raw API responses
solver
{
"reasoning": "SGF11 is a subunit of the SAGA (Spt-Ada-Gcn5-Acetyltransferase) complex, specifically within its deubiquitylase (DUB) module, where it activates the Ubp8 deubiquitylase to remove monoubiquitin from histone H2B. H2B ubiquitination (H2Bub1) is a mark associated with transcriptional elongation and has been linked to chromatin regulation relevant to aging. Loss of H2Bub1 via SGF11/Ubp8 activity alters the epigenetic landscape in ways that can promote gene expression changes detrimental to longevity. In yeast, deletion of SAGA DUB module components, including SGF11, has been associated with extended replicative lifespan, suggesting that SGF11's normal function (promoting H2B deubiquitylation) is anti-longevity. The zinc ion binding activity is consistent with SGF11's structural role in coordinating the DUB module via a zinc finger domain essential for Ubp8 activation. Thus, SGF11's normal enzymatic activator role within SAGA opposes longevity by modulating histone ubiquitination states and downstream transcriptional programs.",
"confidence": 0.65,
"key_pathways": [
"SAGA DUB module / H2B deubiquitylation",
"Histone H2B ubiquitination (H2Bub1) regulation",
"Epigenetic chromatin remodeling and transcriptional coactivation"
],
"mechanism_class": "epigenetic_alterations",
"longevity_influence": "anti_longevity"
}advisor
{
"notes": "The model correctly predicted SGF11 as anti_longevity. The mechanistic reasoning is detailed and accurate: SGF11 is indeed part of the SAGA DUB module, activates Ubp8 deubiquitylase, removes monoubiquitin from H2B, and deletion of SGF11 extends replicative lifespan in yeast. The zinc finger domain role is correctly noted. The confidence of 0.65 is reasonable given the specificity of the knowledge required. Overall, this is an excellent prediction with correct answer and correct mechanism.",
"failure_mode": "correct",
"answer_correct": true,
"mechanism_correct": true,
"reasoning_quality": 5,
"ground_truth_questionable": false
}