Ski2-like RNA helicase structures: common themes and complex assemblies

Abstract

Ski2-like RNA helicases are large multidomain proteins involved in a variety of RNA processing and degradation events. Recent structures of Mtr4, Ski2 and Brr2 provide our first view of these intricate helicases. Here we review these structures, which reveal a conserved ring-like architecture that extends beyond the canonical RecA domains to include a winged helix and ratchet domain. Comparison of apo- and RNA-bound Mtr4 structures suggests a role for the winged helix domain as a molecular hub that coordinates RNA interacting events throughout the helicase. Unique accessory domains provide expanded diversity and functionality to each Ski2-like family member. A common theme is the integration of Ski2-like RNA helicases into larger protein assemblies. We describe the central role of Mtr4 and Ski2 in formation of complexes that activate RNA decay by the eukaryotic exosome. The current structures provide clues into what promises to be a fascinating view of these dynamic assemblies.

Keywords: Brr2; Mtr4; RNA helicase; RNA processing; Ski2; structure.

Figure 1. Members of the Ski2-like helicase family share a common four domain helicase core. (A). Schematic representations (top row) highlight the architectural arrangement of the Ski2-like helicases for the Brr2, Mtr4 and Ski2 RNA helicases and the related Hel308 DNA helicase. Representative structures are also indicated (middle and bottom rows). The helicase core is composed of the RecA1, RecA2, Winged Helix (WH) and Ratchet domains (white lettering). Accessory domains are also indicated (black lettering). Brr2 contains two helicase core cassettes. The current Brr2 structures are limited to the second Brr2 Sec63 domain (composed of the ratchet, HhH and FN3 domains). (B) Domain organization for the Ski2-like helicases. Amino acid residue numbers are from S. cerevisiae, except for Hel308 (A. fulgidus) and DDX60 (H. sapiens). DNA or RNA helicase activity has not been demonstrated for DDX60, although it has been shown to bind both DNA and RNA. Uncharacterized N-terminal regions are not indicated in (A) but are included in (B) as gray boxes. Structures were rendered using PyMol.

Figure 2. Comparison of Mtr4 and Ski2. The structures of Mtr4 (A) and Ski2 (B) are shown from a side-view and top-view (PDB ID 2XGJ and 4A4Z, respectively). For clarity, the arch domain has been removed in the top-view. Domain names and important structural features are indicated, including alternative nomenclature used in the literature.

Figure 3. Substrate binding induces conformational changes in Mtr4. (A) Comparison of the apo (gray) and RNA/ADP bound (color) Mtr4 structures (left panel). Alignment was performed by superimposing the winged helix domains. The cartoon rendition (middle panel) highlights domain motions with respect to the winged helix. Covalent linkages connecting the winged helix to the RecA2, arch and ratchet domains are indicated (black lines). The winged helix also stacks with RecA1. The right panel depicts RNA interactions with the RecA (observed), arch (predicted) and ratchet domains (observed), demonstrating the ability of Mtr4 to interact with every region of the unwinding RNA (i.e., duplex, fork, ssRNA backbone and bases). The winged helix is physically linked to each of the other domains (considering the RecA domains as a single module), suggesting a potential role as a molecular hub that coordinates motions between the other domains. (B) Comparison of the RecA2 and ratchet domains in the apo and substrate-bound structures. Structures were aligned as in (A). The Arch, WH and most of RecA1 are removed for clarity. The ratchet helix, motifs Ia, Ib, IV, and V and the β-hairpin collapse toward the RNA substrate upon binding. Conformational shifts are depicted with black arrows and labeled with observed distances. Phosphates are colored the same as interacting helicase motifs. (C) Superposition of the arch domains (left) indicates that the arms adopt a rigid structure. Comparison of the arch domain when the winged helix domains are aligned (right) highlights conformational differences upon substrate binding. The right view includes apo (white) and both molecules from the RNA-bound structure (green and dark gray).

Figure 4. Exosome activating complexes are mediated by Mtr4 and Ski2. Existing crystal structures are indicated (see text for details). Exosome structures also exist,^-, but are not shown.