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

• Type of Material: Article
• Authors: Maria C. Sterrett, Emory University; Lauryn Cureton, Emory University; Lauren N. Cohen, Emory University; Ambro van Hoof, University of Texas, Houston; Sohail Khoshnevis, Emory University; Milo Fasken, Emory University; Anita Corbett, Emory University; Homa Ghalei, Emory University
• Language: English
• Date: 2023-10-19
• Publisher: NIH
• Publication Version: Preprint (Prior to Peer Review)
• Copyright Statement: The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
• License: Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International
• Final Published Version (URL): https://doi.org/10.1101/2023.10.18.562946
• Title of Journal or Parent Work: bioRxiv
• Start Page: 562946
• Grant/Funding Information: This work was supported by NIH awards R35GM138123 to H.G., R35GM141710 to AvH, and R01GM130147 to AvH and AHC, as well as funds from a Synergy II Nexus Award provided by the Woodruff Health Sciences Center (WHSC), Emory School of Medicine, the Office of the Provost, and Emory College of Arts and Sciences (ECAS) to H.G. and A.H.C. M.C.S. was supported by an F31 grant from the National Institutes of Health. L.A.C. was supported by NIH T32GM149422.
• Keywords: disease model; budding yeast disease model; RNA exosomopathy; translation dysregulation; RNA exosome
• Research Categories: Biology, Molecular; Biology, Genetics; Biology, Neuroscience

Abstract

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.