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

The 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 distinct in vivo consequences. To investigate these functional consequences and distinguish whether they are unique to each RNA exosomopathy mutation, we generated a collection of in vivo models using budding yeast by introducing pathogenic missense mutations in orthologous S. cerevisiae genes. We then performed a comparative RNA-seq analysis to assess broad transcriptomic changes in each mutant model. Three of the mutant models rrp4-G226D, rrp40-W195R and rrp46-L191H, which model mutations in the genes encoding structural subunits of the RNA exosome, EXOSC2, EXOSC3 and EXOSC5 showed 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 in in vivo consequences that are both unique and shared across each variant, providing more insight into the biology underlying each distinct pathology.RNA外切酶体（RNA exosome）是一类进化保守的外切核糖核酸酶复合物，由3个亚基构成的帽子结构、6个亚基组成的桶状核心，以及1个催化性基础亚基所组成。编码RNA外切酶体结构亚基的基因发生错义突变，可引发一类不断增多的多病理表型疾病，统称为RNA外切酶体病（RNA exosomopathies）。该类疾病的症状表现多样，可出现神经系统缺陷或发育异常。RNA外切酶体病的病理多样性提示，结构基因上的不同错义突变会在体内引发截然不同的效应。为探究这些功能效应，并明确其是否为每种RNA外切酶体病突变所特有，我们通过在酿酒酵母（S. cerevisiae）的同源基因中引入致病性错义突变，构建了一系列体内模型。随后我们开展了对比性RNA测序（RNA-seq）分析，以评估各突变模型中的广泛转录组变化。其中，模拟RNA外切酶体结构亚基编码基因EXOSC2、EXOSC3和EXOSC5突变的三种突变模型rrp4-G226D、rrp40-W195R及rrp46-L191H，展现出最为显著的转录组差异。进一步分析显示，这三种突变模型中均存在富集于翻译或核糖体RNA修饰/加工通路的上调转录本。针对突变对翻译过程影响的研究发现，三者在核糖体生物发生方面存在共通缺陷，但对翻译过程的影响却各不相同。综上，本研究首次对多种RNA外切酶体病突变模型开展了对比分析，结果表明不同的RNA外切酶体病突变所引发的体内效应兼具突变特异性与共通性，为解析每种独特病理表型背后的生物学机制提供了新的认知。