YDC1
S. cerevisiae
alkaline dihydroceramidase
What the model saw
Gene: YDC1 Organism: Saccharomyces cerevisiae Known functions: alkaline dihydroceramidase. N-acylsphingosine amidohydrolase activity.
View unredacted entry
alkaline dihydroceramidase. N-acylsphingosine amidohydrolase activity.
Solver output
YDC1 encodes an alkaline dihydroceramidase (N-acylsphingosine amidohydrolase) that hydrolyzes dihydroceramide into sphingosine and fatty acid, thereby reducing cellular ceramide levels. Ceramide is a pro-apoptotic and pro-senescence bioactive sphingolipid in yeast; elevated ceramide promotes growth arrest and cell death, while its reduction by YDC1 activity shifts the sphingolipid rheostat toward sphingosine and away from ceramide. However, ceramide also plays a protective role in stress responses and has been linked to lifespan extension in yeast — loss of ceramide synthesis or excess ceramide catabolism is associated with shortened chronological lifespan. By catabolizing dihydroceramide, YDC1 reduces the pool of ceramide available for pro-longevity signaling (e.g., via Sit4 phosphatase and TORC1 inhibition), thus its normal activity is predicted to be anti-longevity. This places YDC1 in the sphingolipid signaling arm of nutrient/stress sensing pathways that modulate aging.
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 anti_longevity for YDC1. The mechanistic reasoning is sound: YDC1 encodes an alkaline dihydroceramidase that catabolizes dihydroceramide, reducing ceramide levels. The model correctly identifies that ceramide has pro-longevity roles in yeast (via stress signaling, TORC1 inhibition, etc.), so YDC1 activity that depletes ceramide would be anti-longevity. The mechanism class of "altered_intercellular_communication" is somewhat questionable — sphingolipid metabolism/signaling would be more accurate — but the core biochemical reasoning about ceramide's role in yeast longevity is correct. Confidence of 0.65 is appropriately calibrated given the complexity of sphingolipid biology.
Raw API responses
solver
{
"reasoning": "YDC1 encodes an alkaline dihydroceramidase (N-acylsphingosine amidohydrolase) that hydrolyzes dihydroceramide into sphingosine and fatty acid, thereby reducing cellular ceramide levels. Ceramide is a pro-apoptotic and pro-senescence bioactive sphingolipid in yeast; elevated ceramide promotes growth arrest and cell death, while its reduction by YDC1 activity shifts the sphingolipid rheostat toward sphingosine and away from ceramide. However, ceramide also plays a protective role in stress responses and has been linked to lifespan extension in yeast — loss of ceramide synthesis or excess ceramide catabolism is associated with shortened chronological lifespan. By catabolizing dihydroceramide, YDC1 reduces the pool of ceramide available for pro-longevity signaling (e.g., via Sit4 phosphatase and TORC1 inhibition), thus its normal activity is predicted to be anti-longevity. This places YDC1 in the sphingolipid signaling arm of nutrient/stress sensing pathways that modulate aging.",
"confidence": 0.65,
"key_pathways": [
"sphingolipid metabolism",
"ceramide signaling",
"chronological lifespan regulation"
],
"mechanism_class": "altered_intercellular_communication",
"longevity_influence": "anti_longevity"
}advisor
{
"notes": "The model correctly predicted anti_longevity for YDC1. The mechanistic reasoning is sound: YDC1 encodes an alkaline dihydroceramidase that catabolizes dihydroceramide, reducing ceramide levels. The model correctly identifies that ceramide has pro-longevity roles in yeast (via stress signaling, TORC1 inhibition, etc.), so YDC1 activity that depletes ceramide would be anti-longevity. The mechanism class of \"altered_intercellular_communication\" is somewhat questionable — sphingolipid metabolism/signaling would be more accurate — but the core biochemical reasoning about ceramide's role in yeast longevity is correct. Confidence of 0.65 is appropriately calibrated given the complexity of sphingolipid biology.",
"failure_mode": "correct",
"answer_correct": true,
"mechanism_correct": true,
"reasoning_quality": 4,
"ground_truth_questionable": false
}