In vivo characterization of the critical interaction between the RNA exosome and the essential RNA helicase Mtr4 in Saccharomyces cerevisiae

• Type of Material: Article
• Authors: Maria C. Sterrett, Emory University; Daniela Farchi, Emory University; Sarah E. Strassler, Emory University; Lawrence H. Boise, Emory University; Milo B. Fasken, Emory University; Anita H. Corbett, Emory University
• Language: English
• Date: 2023-03-02
• Publisher: Oxford University Press
• Publication Version: Final Published Version
• Copyright Statement: © The Author(s) 2023.
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): https://doi.org/10.1093/g3journal/jkad049
• Title of Journal or Parent Work: G3: Genes, Genomes, Genetics
• Volume: 13
• Issue: 8
• Start Page: jkad049
• Grant/Funding Agency: National Institutes of Health; Emory University; National Cancer Institute; Genetics Society of America; National Science Foundation
• Grant/Funding Information: This work was supported by National Institutes of Health (NIH) R01 grants (GM058728) and the NIH-funded Emory Initiative for Maximizing Student Development (R25 GM099644) to A.H.C. and National Cancer Institute (NCI) R21 grant (CA273773) to L.H.B. M.C.S. was supported by a National Institute of General Medical Sciences (NIGMS) F31 grant (GM134649-01). S.E.S. was supported by the National Science Foundation (NSF) Graduate Research Fellowship (GRFP 1937971). Lastly, we would also like to thank the Genetics Society of America and the Saccharomyces Genomic Database (SGD) (Cherry et al. 2012) for providing community resources and support for scientific discovery.
• Keywords: Rrp4; RNA helicase; EXOSC2; Mtr4; RNA processing; multiple myeloma; RNA exosome
• Subject - Topics: Genomes; Multiple myeloma

Abstract

The RNA exosome is a conserved molecular machine that processes/degrades numerous coding and non-coding RNAs. The 10-subunit complex is composed of three S1/KH cap subunits (human EXOSC2/3/1; yeast Rrp4/40/Csl4), a lower ring of six PH-like subunits (human EXOSC4/7/8/9/5/6; yeast Rrp41/42/43/45/46/Mtr3), and a singular 3′-5′ exo/endonuclease DIS3/Rrp44. Recently, several disease-linked missense mutations have been identified in structural cap and core RNA exosome genes. In this study, we characterize a rare multiple myeloma patient missense mutation that was identified in the cap subunit gene EXOSC2. This missense mutation results in a single amino acid substitution, p.Met40Thr, in a highly conserved domain of EXOSC2. Structural studies suggest that this Met40 residue makes direct contact with the essential RNA helicase, MTR4, and may help stabilize the critical interaction between the RNA exosome complex and this cofactor. To assess this interaction in vivo, we utilized the Saccharomyces cerevisiae system and modeled the EXOSC2 patient mutation into the orthologous yeast gene RRP4, generating the variant rrp4-M68T. The rrp4-M68T cells show accumulation of certain RNA exosome target RNAs and show sensitivity to drugs that impact RNA processing. We also identified robust negative genetic interactions between rrp4-M68T and specific mtr4 mutants. A complementary biochemical approach revealed that Rrp4 M68T shows decreased interaction with Mtr4, consistent with these genetic results. This study suggests that the EXOSC2 mutation identified in a multiple myeloma patient impacts the function of the RNA exosome and provides functional insight into a critical interface between the RNA exosome and Mtr4.