The EF-G-like GTPase Snu114p regulates spliceosome dynamics mediated by Brr2p, a DExD/H box ATPase - PubMed (original) (raw)

The EF-G-like GTPase Snu114p regulates spliceosome dynamics mediated by Brr2p, a DExD/H box ATPase

Eliza C Small et al. Mol Cell. 2006.

Abstract

Binding of a pre-mRNA substrate triggers spliceosome activation, whereas the release of the mRNA product triggers spliceosome disassembly. The mechanisms that underlie the regulation of these rearrangements remain unclear. We find evidence that the GTPase Snu114p mediates the regulation of spliceosome activation and disassembly. Specifically, both unwinding of U4/U6, required for spliceosome activation, and disassembly of the postsplicing U2/U6.U5.intron complex are repressed by Snu114p bound to GDP and derepressed by Snu114p bound to GTP or nonhydrolyzable GTP analogs. Further, similar to U4/U6 unwinding, spliceosome disassembly requires the DExD/H box ATPase Brr2p. Together, our data define a common mechanism for regulating and executing spliceosome activation and disassembly. Although sequence similarity with EF-G suggests Snu114p functions as a molecular motor, our findings indicate that Snu114p functions as a classic regulatory G protein. We propose that Snu114p serves as a signal-dependent switch that transduces signals to Brr2p to control spliceosome dynamics.

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Figures

Figure 1

Purification of in vivo Assembled Spliceosomes Poised for Disassembly (A) Prp43p- and Prp22p-associated spliceosomes, affinity-purified from yJPS797 or yJPS773 using a tandem affinity purification (TAP) tag (Rigaut et al., 1999), are enriched for U2, U5 and U6. RNA was extracted from lysate (L) or purified spliceosomes (P); 1% or 100%, respectively, was analyzed by primer extension (top). The percent yield for each snRNA is shown for Prp43p-(black) and Prp22p-(grey) associated spliceosomes (bottom). (B) Prp43p-associated spliceosomes are enriched specifically for excised intron, whereas Prp22p-associated spliceosomes are enriched for excised intron and ligated exons. RNA was extracted from lysate (L) or purified spliceosomes (P); 0.4% or 100%, respectively, was probed by Northern for the U3A pre-snoRNA, snoRNA and excised intron, indicated from top to bottom on the left. (C) In Prp43p-associated spliceosomes, the U3A intron is branched. RNA extracted from spliceosomes was incubated without (-) or with (+) debranchase (Dbr1p), as described (Khalid et al., 2005) for 30 min at 22°C, and probed by Northern for the branched and debranched introns, depicted from top to bottom on the left. (D) In Prp43p-associated spliceosomes, U2 crosslinks with U6. After UV-irradiating spliceosomes, RNA was extracted and probed sequentially by Northern for U6, U2 and U5, as indicated below the blots. The crosslinked species is indicated as U2/U6.

Figure 2

Prp43p-associated Spliceosomes Disassemble in an ATP- and Prp43p-Dependent Manner (A) A Prp43p-associated U2/U6•U5•intron complex disassembles rapidly in the presence of ATP. Complexes were purified from yJPS797 and incubated at 4°C in the presence (+) or absence (-) of ATP. At the indicated times, samples from the reactions were quenched and then analyzed by native gel followed by serial Northern probing. The migration of the U2/U6•U5•intron complex; the free U3A intron, and the free U6, U2 and U5 snRNAs are indicated on the left. (B) Disassembly of the U2/U6•U5•intron complex requires hydrolyzable ATP. Reactions were incubated at 4°C for 60 s and analyzed as in (A). (C) Disassembly of the U2/U6•U5•intron complex is promoted preferentially by ATP. Complexes were incubated at 4°C and analyzed as in (A). (D) ATP does not promote disassembly of Prp22p-associated spliceosomes. Prp43p-associated U2/U6•U5•intron complexes, purified from yJPS797, and Prp22p-associated U2/U6•U5•intron•mRNA complexes, purified from yJPS773, were incubated and analyzed as in (B). (E) Disassembly of Prp43p-associated spliceosomes is inhibited by the prp43-Q423N mutation but not by the prp22-G810A mutation. Spliceosomes were purified from wild-type PRP43 (yJPS797) or PRP22 (yJPS1049) and mutant prp43-Q423N (yJPS798) or prp22-G810A (yJPS1052) and then incubated and analyzed as in (B).

Figure 3

Spliceosome Disassembly Requires the DExD/H-box ATPase Brr2p (A) Disassembly of Prp43p-associated spliceosomes is inhibited by brr2 mutations. Spliceosomes were purified from the wild-type strain BRR2 (yJPS999) or the mutant strains brr2-1 (yJPS1000) and brr2-R1107A (yJPS1001). Spliceosomes were incubated and analyzed as in Figure 2B. (B) As for brr2-1, the mutant brr2-R1107A is cold sensitive. Cells were diluted from liquid culture and grown on rich media for 2 days at 30°C or 6 days at 15°C. (C) In brr2 mutants, the excised lariat intron from U3A accumulates. Wild-type BRR2 (yJPS999) or the mutants brr2-1 (yJPS1000) and brr2-R1107A (yJPS1001) were grown in rich liquid media at 30°C and shifted to 15°C for 4 h. RNA was analyzed by Northern as in Figure 1B.

Figure 4

Spliceosome Disassembly is Promoted and Regulated by the GTPase Snu114p (A) Disassembly of Prp43p-associated spliceosomes is inhibited by snu114 mutants. Spliceosomes were purified from the wild-type strain SNU114 (yJPS1053) or the mutant strains snu114-14 (yJPS1120) and snu114-60 (yJPS1056). Spliceosomes were incubated and analyzed as in Figure 2E. (B) prp43 and snu114 mutants genetically interact. yTB135 was cotransformed with plasmids encoding PRP43 (pJPS1346) or prp43-Q423N (pJPS1347) and SNU114 (pTB106), snu114-14 (pTB108) or snu114-60 (pTB113), grown in liquid media, diluted and grown on solid media containing 5-fluoroorotic acid for 5 days at 30°C. (C) Spliceosome disassembly is repressed specifically by GDP and derepressed specifically by GTP. Prp43p-associated spliceosomes, purified from a wild-type strain (yJPS797), were incubated at 4°C for 60 s and analyzed as in Figure 2B. (D) Spliceosome disassembly is regulated by Snu114p. Prp43p-associated spliceosomes were purified from a wild-type strain (yJPS1053) or a snu114-D271N mutant strain (yJPS1054) that appears to switch the specificity of Snu114p from guanine to xanthine (Bartels et al., 2003). Spliceosomes were incubated and analyzed as in Figure 2B. ATP, GDP and XDP concentrations were 2 mM; GTP and XTP concentrations were 0.5 mM. (E) Spliceosome disassembly does not require GTP hydrolysis. Prp43p-associated spliceosomes, purified from wild-type SNU114 (yJPS1053) or mutant snu114-D271N (yJPS1054), were incubated at 4°C for 60 s and analyzed as in Figure 2B.

Figure 5

U4/U6 Unwinding is Regulated by Snu114p (A) Purification of U4/U6•U5 snRNPs associated with Prp28p. U4/U6•U5 snRNPs were affinity purified from lysates of yJPS1004 after glycerol gradient fractionation. By primer extension, RNA was analyzed from lysate (L) and pooled glycerol gradient fractions (F) and after immunoprecipitation from the supernatant (S) and the purified snRNP (P). (B) U4/U6 unwinding is repressed specifically by GDP and derepressed specifically by GTP. Prp28p-associated U4/U6•U5 snRNPs were incubated at 4°C and quenched after 60 s. RNA was extracted at 4°C, resolved on a native RNA gel and analyzed by Northern, probing simultaneously for U4 and U6. The migration of base paired U4/U6 and free U4 and U6 are indicated to the left. (C) U4/U6 unwinding is regulated by Snu114p. Prp28p-associated U4/U6•U5 snRNPs were purified from wild-type SNU114 (yJPS1108) or mutant snu114-D271N (yJPS1111). Nucleotide concentrations were as in Figure 4D. snRNPs were incubated and analyzed as in (B). (D) U4/U6 unwinding does not require GTP hydrolysis. Prp28p-associated U4/U6•U5 snRNPs purified from wild-type SNU114 (yJPS1108) or mutant snu114-D271N (yJPS1111) were incubated and analyzed as in (B). (E) U4/U6 unwinding requires the first Sec63 domain of Brr2p. Prp28p-associated U4/U6•U5 snRNPs were purified from a wild-type BRR2 (yJPS1115) or mutant brr2-R1107A (yJPS1117) strain and incubated and analyzed as in (B).

Figure 6

A Role for Snu114p in Regulating Brr2p-dependent Spliceosome Dynamics A simplified splicing cycle is shown, depicting the stages of spliceosome binding and activation (left) and splicing and spliceosome disassembly (right). A model for the roles of Snu114p and Brr2p is illustrated. In the model, Snu114p acts as switch that turns Brr2p “on” and “off”. In the GTP state, Snu114p turns Brr2p “on” to trigger spliceosome activation and disassembly (upper left and lower right, respectively). In the GDP state, Snu114p turns Brr2p “off” to repress inappropriate RNA rearrangements (lower left, upper right). GTP hydrolysis and exchange of GDP for GTP serves to toggle the switch, signaling transitions in the splicing cycle that require up- or down-regulation of Brr2p. See Discussion for details.

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The EF-G-like GTPase Snu114p regulates spliceosome dynamics mediated by Brr2p, a DExD/H box ATPase - PubMed (original) (raw)