Comparative analyses of disease-linked missense mutations in the RNA exosome modeled in budding yeast reveal distinct functional consequences in translation

Abstract

ABSTRACTThe RNA exosome is an evolutionarily conserved exoribonuclease complex that consists of a 3- subunit cap, a 6-subunit barrel-shaped core, and a catalytic base subunit. Missense mutations in genes encoding structural subunits of the RNA exosome cause a growing family of diseases with diverse pathologies, collectively termed RNA exosomopathies. The disease symptoms vary and can manifest as neurological defects or developmental disorders. The diversity of the RNA exosomopathy pathologies suggests that the different missense mutations in structural genes result in distinctin vivoconsequences. To investigate these functional consequences and distinguish whether they are unique to each RNA exosomopathy mutation, we generated a collection ofin vivomodels using budding yeast by introducing pathogenic missense mutations in orthologousS. cerevisiaegenes. We then performed a comparative RNA-seq analysis to assess broad transcriptomic changes in each mutant model. Three of the mutant modelsrrp4-G226D, rrp40-W195Randrrp46-L191H, which model mutations in the genes encoding structural subunits of the RNA exosome,EXOSC2, EXOSC3andEXOSC5showed the largest transcriptomic differences. Further analyses revealed shared increased transcripts enriched in translation or ribosomal RNA modification/processing pathways across the three mutant models. Studies of the impact of the mutations on translation revealed shared defects in ribosome biogenesis but distinct impacts on translation. Collectively, our results provide the first comparative analysis of several RNA exosomopathy mutant models and suggest that different RNA exosomopathy mutations result inin vivoconsequences that are both unique and shared across each variant, providing more insight into the biology underlying each distinct pathology.