Targeting RNA for processing or destruction by the eukaryotic RNA exosome and its cofactors

Abstract

The eukaryotic RNA exosome is an essential and conserved protein complex that can degrade or process RNA substrates in the 3'-to-5' direction. Since its discovery nearly two decades ago, studies have focused on determining how the exosome, along with associated cofactors, achieves the demanding task of targeting particular RNAs for degradation and/or processing in both the nucleus and cytoplasm. In this review, we highlight recent advances that have illuminated roles for the RNA exosome and its cofactors in specific biological pathways, alongside studies that attempted to dissect these activities through structural and biochemical characterization of nuclear and cytoplasmic RNA exosome complexes.

Keywords: 3′ to 5′; RNA degradation; RNA exosome; RNA processing; endoribonuclease; exoribonuclease; exosome.

Figure 1.

RNA paths and Dis3 conformations in the yeast nuclear exosome. (A) Domain schematics for S. cerevisiae nuclear exosome components. Catalytic sites are represented by stars, and amino acid lengths for the S. cerevisiae proteins are indicated. (B) Direct access conformation of Dis3. Dis3 and the Rrp6 exosome-associated region (EAR) domain are from Protein Data Bank (PDB) 5K36. The central channel is indicated by black dashed lines, including a speculative path to the Dis3 endonuclease site, and RNA is represented as a red line with the 5′ end indicated. (C) Through-channel conformation of Dis3. Dis3 is from PDB 4IFD, and the Rrp6 EAR domain is from PDB 5K36. RNA and the central channel are indicated as previously, with the dashed red line representing a speculative RNA path to the Dis3 endo active site. (D) Rrp6 catalytic module (from PDB 5K36) bound to the core with RNA in its active site. The RNA path to Rrp6 is based on biochemical data and PDB 5K36.

Figure 2.

The TRAMP complex and the nuclear exosome. (A) Domain schematics for S. cerevisiae C1D, Mpp6, and TRAMP components. Catalytic sites are indicated by stars, and amino acid lengths for the S. cerevisiae proteins are shown. (B) Structural models for the nuclear exosome and associated cofactors, with RNA omitted for clarity. Black dotted lines represent connecting regions for which no structural information is available. Mtr4 and Trf4/Air2 peptides are from PDB 4U4C; Trf4/Air2 zinc knuckles are from PDB 3NYB; the PH-like ring, Rrp40, Rrp4, Csl4, Dis3, the Rrp6 catalytic module, and the Rrp6 EAR are from PDB 5K36; the Rrp6 PMC2NT domain, C1D, and the Mtr4 N-terminal peptide are from PDB 4WFD and were positioned based on PDB 5C0W. (C) Model for Mtr4 threading of RNA to the nuclear exosome after polyadenylation by Trf4/5. The central channel is indicated by black dashed lines, and RNA is represented as a red line with the 5′ end indicated. Dashed red arrows represent RNA paths to the catalytic subunits. Helicase direction is indicated by a gear and arrow.

Figure 3.

The Ski complex and the cytoplasmic exosome. (A) Domain schematics for S. cerevisiae Ski complex components. Catalytic sites are represented by stars, and amino acid lengths for the S. cerevisiae proteins are shown. (B) Structural models for the cytoplasmic exosome and associated cofactors, with RNA omitted for clarity. Black dotted lines represent connecting regions for which no structural information is available. The Ski3, Ski8, and Ski2 N termini are from PDB 4BUJ; the Ski2 globular region and insertion are from PDB 4A4Z and were aligned to PDB 4BUJ; the Ski7 CTDs are from PDB 4ZKE; the PH-like ring, Rrp40, Rrp4, Csl4, Dis3, and the Ski7 EAR are from PDB 5JEA. (C) Model for Ski complex channeling of a translating mRNA to the cytoplasmic exosome. The central channel is indicated by black dashed lines, and RNA is represented as a red line with the 3′ end shown bound to the Rrp44 exonuclease active site. Helicase direction is indicated by a gear and arrow.

Figure 4.

AIM–Arch interactions recruit the exosome for rRNA processing (A) Schematic for the S. cerevisiae 7-kb pre-rRNA molecule. Regions of the RNA contained within the mature ribosome are shown as boxes, and spacers are shown as lines. The direction of transcription is shown with an arrow, and A₀ and C₂ endonucleolytic cleavage sites are indicated. (B) Schematic for a mature ribosome. (C) A Utp18_AIM–Mtr4_Arch interaction recruits the exosome for 5′ externally transcribed spacer (ETS) removal after endonucleolytic cleavage at the A₀ site. (D) A Nop53_AIM–Mtr4_Arch interaction recruits the exosome for 5.8S rRNA processing after Las1 cleavage at the C₂ site.