DIE2
S. cerevisiae
dolichyl-P-Glc:Glc(2)Man(9)GlcNAc(2)-PP-dolichol alpha-1,2- glucosyltransferase
What the model saw
Gene: DIE2 Organism: Saccharomyces cerevisiae Known functions: dolichyl-P-Glc:Glc(2)Man(9)GlcNAc(2)-PP-dolichol alpha-1,2- glucosyltransferase. dolichyl pyrophosphate Glc2Man9GlcNAc2 alpha-1,2-glucosyltransferase activity. dolichyl-phosphate-glucose-glycolipid alpha-glucosyltransferase activity.
View unredacted entry
dolichyl-P-Glc:Glc(2)Man(9)GlcNAc(2)-PP-dolichol alpha-1,2- glucosyltransferase. dolichyl pyrophosphate Glc2Man9GlcNAc2 alpha-1,2-glucosyltransferase activity. dolichyl-phosphate-glucose-glycolipid alpha-glucosyltransferase activity.
Solver output
DIE2 encodes the alpha-1,2-glucosyltransferase responsible for adding the third glucose residue to the dolichol-linked oligosaccharide precursor (Glc2Man9GlcNAc2-PP-dolichol → Glc3Man9GlcNAc2-PP-dolichol) during N-linked glycosylation in the ER. This fully glucosylated precursor is the obligate substrate for transfer to nascent polypeptides by the oligosaccharyltransferase complex. Proper N-glycosylation is essential for the calnexin/calreticulin folding cycle and ER quality control; loss of DIE2 function impairs protein folding fidelity and triggers chronic ER stress. Sustained ER stress activates the unfolded protein response (UPR) and, if unresolved, promotes proteotoxicity and premature cellular aging. Intact N-glycosylation machinery therefore supports proteostasis, a key pro-longevity mechanism, by ensuring correct protein folding and preventing accumulation of misfolded proteins.
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 predicted pro_longevity with 0.72 confidence, but the ground truth is anti_longevity. DIE2 is classified as anti-longevity in GenAge, meaning its deletion or loss extends lifespan (i.e., the gene normally shortens lifespan). The model's reasoning assumed that because DIE2 supports proper N-glycosylation and proteostasis, it must be pro-longevity. However, this logic is flawed — the GenAge classification of anti_longevity means that DIE2 activity works against longevity (its deletion extends lifespan). The model confused the direction of the effect: it reasoned that intact glycosylation machinery supports proteostasis (true in principle), but failed to consider that DIE2 might promote aging through mechanisms such as ER stress induction or other pathways. The mechanistic reasoning was also incorrect in its conclusion — it assumed loss of DIE2 would be harmful, when in fact loss of DIE2 appears to extend lifespan. The model was confidently wrong in both the classification and the mechanistic interpretation.
Raw API responses
solver
{
"reasoning": "DIE2 encodes the alpha-1,2-glucosyltransferase responsible for adding the third glucose residue to the dolichol-linked oligosaccharide precursor (Glc2Man9GlcNAc2-PP-dolichol → Glc3Man9GlcNAc2-PP-dolichol) during N-linked glycosylation in the ER. This fully glucosylated precursor is the obligate substrate for transfer to nascent polypeptides by the oligosaccharyltransferase complex. Proper N-glycosylation is essential for the calnexin/calreticulin folding cycle and ER quality control; loss of DIE2 function impairs protein folding fidelity and triggers chronic ER stress. Sustained ER stress activates the unfolded protein response (UPR) and, if unresolved, promotes proteotoxicity and premature cellular aging. Intact N-glycosylation machinery therefore supports proteostasis, a key pro-longevity mechanism, by ensuring correct protein folding and preventing accumulation of misfolded proteins.",
"confidence": 0.72,
"key_pathways": [
"N-linked glycosylation / dolichol pathway",
"ER protein quality control / calnexin-calreticulin cycle",
"Unfolded protein response (UPR)"
],
"mechanism_class": "loss_of_proteostasis",
"longevity_influence": "pro_longevity"
}advisor
{
"notes": "The model predicted pro_longevity with 0.72 confidence, but the ground truth is anti_longevity. DIE2 is classified as anti-longevity in GenAge, meaning its deletion or loss extends lifespan (i.e., the gene normally shortens lifespan). The model's reasoning assumed that because DIE2 supports proper N-glycosylation and proteostasis, it must be pro-longevity. However, this logic is flawed — the GenAge classification of anti_longevity means that DIE2 activity works against longevity (its deletion extends lifespan). The model confused the direction of the effect: it reasoned that intact glycosylation machinery supports proteostasis (true in principle), but failed to consider that DIE2 might promote aging through mechanisms such as ER stress induction or other pathways. The mechanistic reasoning was also incorrect in its conclusion — it assumed loss of DIE2 would be harmful, when in fact loss of DIE2 appears to extend lifespan. The model was confidently wrong in both the classification and the mechanistic interpretation.",
"failure_mode": "confident_wrong",
"answer_correct": false,
"mechanism_correct": false,
"reasoning_quality": 2,
"ground_truth_questionable": false
}