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Review
. 2021 Mar;46(3):225-238.
doi: 10.1016/j.tibs.2020.10.006. Epub 2020 Nov 30.

DEAH-Box RNA Helicases in Pre-mRNA Splicing

Francesca De Bortoli  1 , Sara Espinosa  1 , Rui Zhao  2
Affiliations
Review

DEAH-Box RNA Helicases in Pre-mRNA Splicing

Francesca De Bortoli et al. Trends Biochem Sci. 2021 Mar.

Abstract

In eukaryotic cells, pre-mRNA splicing is catalyzed by the spliceosome, a highly dynamic molecular machinery that undergoes dramatic conformational and compositional rearrangements throughout the splicing cycle. These crucial rearrangements are largely driven by eight DExD/H-box RNA helicases. Interestingly, the four helicases participating in the late stages of splicing are all DEAH-box helicases that share structural similarities. This review aims to provide an overview of the structure and function of these DEAH-box helicases, including new information provided by recent cryo-electron microscopy structures of the spliceosomal complexes.

Keywords: DEAH-box RNA helicases; cryo-EM; spliceosome.

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Figures

Figure 1.
Figure 1.
Overall Domain Organization and Structure of the Splicing Helicases. (A) Domain organizations and conserved motifs of the three subfamilies of superfamily 2 (SF2) helicases that the splicing helicases belong to. (B) The structure of Chaetomium thermophilum DEAH-box helicase Prp43 (PDB ID 5LTA) illustrating the domain architecture of DEAH-box helicases using the same color scheme as in A. Abbreviations: HB, helix bundle; HLH, helix–loop–helix; IG, immunoglobulin-like; NTD, N-terminal domain; OB, oligosaccharide-binding fold; WH, winged helix.
Figure 2.
Figure 2.
Structural Basis for the DEAH-Box Mechanism of Action and Regulation by G-Patch Domains. The domains are colored as in Figure 1A. (A) The closed form of Chaetomium thermophilum DEAH-box helicase Prp43 bound to ADP and RNA (PDB ID 5LTA). (B) The open form of C. thermophilum DEAH-box helicase Prp22 bound to RNA (PDB ID 6I3P). Both proteins are shown in the same orientation after aligning their RecA1 domains. The RNA stacked in the binding tunnel is highlighted in red. (C) Location of the ratchet helix in C. thermophilum Prp22 (PDB ID 6I3P). The ratchet helix is highlighted in pink. (D) A zoomed in view of the ratchet helix and its surroundings. Residues on the ratchet helix that interact, or potentially interact, with a longer RNA are shown as sticks. (E) The structure of C. thermophilum Prp2 in complex with Spp2 (purple) (PDB ID 6RM9). (F) The structure of Homo sapiens Prp43 with NKRF (purple) bound (PDB ID 6SH7). Abbreviations: HB, helix bundle; OB, oligosaccharide-binding fold; WH, winged helix.
Figure 3.
Figure 3.
Prp2 in the Spliceosome Bact Complex. (A) Overall structure of the yeast Bact complex (PDB ID 5GM6). (B) A zoomed in view of the region containing Prp2. The black dotted line is the hypothetical path of the pre-mRNA and the teal oval represents the likely location of Spp2. (C) A model depicting SF3b displacement and freeing of the branch point (BP) by Prp2. Abbreviation: CTD, C-terminal domain.
Figure 4.
Figure 4.
Prp16 in the Spliceosome C Complex. (A) Overall structure of the yeast C complex (PDB ID 5LJ5) showing the hypothetical path of the 3′ end of the pre-mRNA that would allow for remodeling by Prp16. (B) C complex rotated by 45° with respect to panel A. The U6 small nuclear RNA (snRNA; orange) does not come close to Prp16 and thus can be ruled out as a target of Prp16. (C) A mechanistic model shows that Prp16 pulls the pre-mRNA, dislodging Cwc25 and Yju2 and leading to destabilization of the U2–BP interaction. Abbreviation: BP, branch point.
Figure 5.
Figure 5.
Prp22 in the Spliceosome P Complex. (A) Overall structure of the yeast P complex (PDB ID 6BK8) with Prp22 located in the periphery. (B) A zoomed in view of the region containing Prp22. Prp22 attaches to the spliceosome through its interaction with Prp8, protein UNK, and the 3′ exon (green). (C) A schematic representation of the winching and 3′ splice site proofreading mechanisms by which Prp22 pulls on and releases the 3′ exon from the spliceosome (adapted from [32]). Abbreviations: BP, branch point; CTD, C-terminal domain.
Figure 6.
Figure 6.
Prp43 in the Spliceosome ILS Complex. (A) Overall structure of the yeast ILS complex (PDB ID 5Y88). The light blue oval represents the likely location of the Ntr1 G-patch with insufficient density for modeling. (B) A zoomed in view of the Prp43-containing region of the ILS complex. Dotted lines indicate the distance from the U6 small nuclear RNA (snRNA) and the pre-mRNA to the Prp43 RNA-binding groove. (C) A model of how Prp43 translocation along the U6 snRNA could lead to spliceosome disassembly (adapted from [79]). Abbreviations: ILS, intron lariat spliceosome; NTC, NineTeen complex; NTR, NTC related.
None
Pre-mRNA Splicing. (A) Schematic representation of the two transesterification reactions in pre-mRNA splicing. Boxes and solid lines represent the exons and introns, respectively. The red arrows show the nucleophilic attacks at the phosphodiester bond at the 5′ and 3′ ss during splicing. (B) A schematic representation of the splicing cycle in yeast is shown in the inside ring. Only the snRNPs (ovals) but not non-snRNP proteins are shown for simplicity. The spliceosomal helicases are indicated in red. The outside ring shows the cryo-EM structure of each corresponding spliceosomal complex and its PDB ID.
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