Overview of pathogenic amino acid substitutions in the human cap subunit EXOSC2 of the RNA exosome. (A) The RNA exosome is an evolutionary conserved ribonuclease complex composed of nine structural subunits (EXOSC1-9) and one catalytic subunit (DIS3) that form a “cap” and “core” ring-like structure. The three-subunit cap at the top of the complex is composed of EXOSC1/Csl4 (Human/S. cerevisiae), EXOSC2/Rrp4, and EXOSC3/Rrp40. The six-subunit core is composed of EXOSC4/Rrp41, EXOSC5/Rrp46, EXOSC6/Mtr3, EXOSC7/Rrp42, EXOSC8/Rrp43, and EXOSC9/Rrp45. The DIS3/Dis3/Rrp44 catalytic subunit is located at the bottom. Missense mutations in the gene encoding the EXOSC2 cap subunit (teal blue, labeled 2) are linked to a novel syndrome termed SHRF (short stature, hearing loss, retinitis pigmentosa and distinctive facies) (Di Donato et al. 2016). In contrast, missense mutations in the gene encoding the EXOSC3 cap subunit (dark blue, labeled 3) cause PCH1b (pontocerebellar hypoplasia type 1b) (Wan et al. 2012; Biancheri et al. 2013; Eggens et al. 2014; Halevy et al. 2014; Schottmann et al. 2017). (B) The structure and organization of the RNA exosome is highly conserved across eukaryotes. A structural model of the human nuclear RNA exosome (left) [PDB 6D6R] (Weick et al. 2018) and the S. cerevisiae nuclear RNA exosome (right) [PDB 6FSZ] (Schuller et al. 2018) are depicted with the cap subunits EXOSC1/Csl4 (Human/S. cerevisiae), EXOSC2/Rrp4, EXOSC3/Rrp40, and catalytic subunit DIS3/Dis3/Rrp44 labeled. (C,D) Domain structures are shown for (C) EXOSC2/Rrp4 and (D) EXOSC3/Rrp40. Each of these cap subunits is composed of three different domains: an amino-terminal domain, a putative RNA binding S1 domain, and a carboxy-terminal putative RNA binding KH (K homology) domain. The “GxNG” motif identified in the KH domain of both cap subunits is boxed in green. The position of the disease-linked amino acid substitutions in human EXOSC2 and EXOSC3 are depicted above the domain structures in red. Sequence alignments of EXOSC2/Rrp4 and EXOSC3/Rrp40 orthologs from Homo sapiens (Hs), Mus musculus (Mm), and S. cerevisiae (Sc) below the domain structures show the highly conserved residues altered in disease in red and the conserved sequences flanking these residues in gray. The amino acid substitutions in S. cerevisiae Rrp4 generated in this study and those in S. cerevisiae Rrp40, described previously (Fasken et al. 2017; Gillespie et al. 2017), that correspond to the disease-linked amino acid substitutions in human EXOSC2 and EXOSC3, are shown below the structures in red.
