"Nought may endure but mutability": spliceosome dynamics and the regulation of splicing

Abstract

The spliceosome is both compositionally and conformationally dynamic. Each transition along the splicing pathway presents an opportunity for progression, pausing, or discard, allowing splice site choice to be regulated throughout both the assembly and catalytic phases of the reaction.

Figure 1. Two-state conformational model of the catalytic spliceosome

Spliceosomal conformations competent to carry out the first and second steps are in competition with one another. In addition, two opposing classes of prp8 alleles modulate an event in the first-to-second step transition distinct from that modulated by alleles of prp16 and U6 snRNA (upper) (Liu et al., 2007); thus, two distinct events (‘opening’ and ‘substrate repositioning’) can be distinguished. Accompanying conformational changes in U2 snRNA stem II (lower) parallel these two events (Hilliker et al., 2007; Perriman and Ares, 2007).

Figure 2. Schematic of RNA:RNA interactions that contribute to the first step of splicing

Pre-mRNA is shown in black, U2 snRNA in red, U5 snRNA in grey, and U6 snRNA in green; numbering corresponds to S. cerevisiae snRNAs and indicates U6 nucleotides discussed in this review. Nucleophilic attack of the 5′SS by BS (the first catalytic step of the splicing reaction) is shown.

Figure 3. NTPase-associated steps during splicing offer opportunities for kinetic discrimination of suboptimal pre-mRNA substrates

(upper) Schematic of transitions facilitated by DExD/H-box ATPases and the Snu114 GTPase during pre-mRNA splicing. SS, splice site; BS, branch site. (lower) Characterised examples of kinetic proofreading mediated by spliceosomal ATPases: (left) Altered competition between BS-U2 pairing and the conformational change mediated by the Prp5 ATPase changes the fidelity of BS selection. (center) Altered competition between the first catalytic step and Prp16 ATPase activity affects the fidelity of splice site usage in this step. (right) Altered competition between the second catalytic step and Prp22 ATPase affects second step splice site fidelity.