RPP2B
S. cerevisiae
ribosomal protein P2 RPP2B
What the model saw
Gene: RPP2B Organism: Saccharomyces cerevisiae Known functions: ribosomal protein P2 RPP2B. molecular function inhibitor activity. protein binding. protein kinase activator activity. structural constituent of ribosome.
View unredacted entry
ribosomal protein P2 RPP2B. molecular function inhibitor activity. protein binding. protein kinase activator activity. structural constituent of ribosome.
Solver output
RPP2B encodes a ribosomal stalk protein (P2B) that is a structural constituent of the large ribosomal subunit and participates in translational elongation by stimulating EF-2/EF-G GTPase activity. As a protein kinase activator, it can activate CK2 (casein kinase 2), which feeds into TOR signaling and promotes anabolic processes. Ribosomal protein genes in yeast are well-established negative regulators of longevity: deletion of many RP genes, particularly those of the large subunit, extends chronological and replicative lifespan by reducing translational output and mimicking dietary restriction through downregulation of the TORC1-driven ribosome biogenesis program. RPP2B's role as a structural ribosome component and kinase activator places it squarely in the nutrient-sensing/TOR axis, where its normal activity promotes growth at the expense of longevity. Reduced ribosomal function and translation rate are consistently pro-longevity interventions in yeast and other model organisms.
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 RPP2B. The mechanistic reasoning is solid and well-grounded: ribosomal protein genes in yeast are well-established negative regulators of longevity, and deletion of large subunit RP genes typically extends lifespan. The model correctly identifies RPP2B as a structural ribosome component and connects it to the TOR/nutrient-sensing axis. The CK2 activation detail is a reasonable addition given RPP2B's known kinase activator activity. The mechanism class "deregulated_nutrient_sensing" is a reasonable fit, though "protein_synthesis/translation" might be more directly accurate. Overall, the reasoning is coherent and the prediction is correct with appropriate confidence (0.72).
Raw API responses
solver
{
"reasoning": "RPP2B encodes a ribosomal stalk protein (P2B) that is a structural constituent of the large ribosomal subunit and participates in translational elongation by stimulating EF-2/EF-G GTPase activity. As a protein kinase activator, it can activate CK2 (casein kinase 2), which feeds into TOR signaling and promotes anabolic processes. Ribosomal protein genes in yeast are well-established negative regulators of longevity: deletion of many RP genes, particularly those of the large subunit, extends chronological and replicative lifespan by reducing translational output and mimicking dietary restriction through downregulation of the TORC1-driven ribosome biogenesis program. RPP2B's role as a structural ribosome component and kinase activator places it squarely in the nutrient-sensing/TOR axis, where its normal activity promotes growth at the expense of longevity. Reduced ribosomal function and translation rate are consistently pro-longevity interventions in yeast and other model organisms.",
"confidence": 0.72,
"key_pathways": [
"TORC1-ribosome biogenesis axis",
"translational elongation (EF-2 GTPase stimulation)",
"CK2 kinase activation"
],
"mechanism_class": "deregulated_nutrient_sensing",
"longevity_influence": "anti_longevity"
}advisor
{
"notes": "The model correctly predicted anti_longevity for RPP2B. The mechanistic reasoning is solid and well-grounded: ribosomal protein genes in yeast are well-established negative regulators of longevity, and deletion of large subunit RP genes typically extends lifespan. The model correctly identifies RPP2B as a structural ribosome component and connects it to the TOR/nutrient-sensing axis. The CK2 activation detail is a reasonable addition given RPP2B's known kinase activator activity. The mechanism class \"deregulated_nutrient_sensing\" is a reasonable fit, though \"protein_synthesis/translation\" might be more directly accurate. Overall, the reasoning is coherent and the prediction is correct with appropriate confidence (0.72).",
"failure_mode": "correct",
"answer_correct": true,
"mechanism_correct": true,
"reasoning_quality": 4,
"ground_truth_questionable": false
}