The spliceosome: caught in a web of shifting interactions

Current Opinion in Structural Biology

Volumn 17, Issue 3, 2007, Pages 310-315

  Valadkhan, Saba ^a  

^a CASE WESTERN RESERVE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

CRYOELECTRON MICROSCOPY; GENE EXPRESSION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION; REVIEW; RNA SPLICING; SPLICEOSOME;

ANIMALS; BINDING SITES; HUMANS; RNA; RNA SPLICING; SPLICEOSOMES;

EUKARYOTA;

EID: 34347400372     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2007.05.001     Document Type: Review

References (35)

1. Will C.L., and Luhrmann R. Spliceosome structure and function. In: Gesteland R.F., Cech T.R., and Atkins J.F. (Eds). The RNA World (2006), Cold Spring Harbor Laboratory Press 369-400
2. Nilsen T.W. RNA-RNA interactions in nuclear pre-mRNA splicing. In: Simons R.W., and Grunberg-Manago M. (Eds). RNA Structure and Function (1998), Cold Spring Harbor Laboratory Press 279-307
3. Staley J.P., and Guthrie C. Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell 92 (1998) 315-326
4. Burgess S.M., and Guthrie C. A mechanism to enhance mRNA splicing fidelity: the RNA-dependent ATPase Prp16 governs usage of a discard pathway for aberrant lariat intermediates. Cell 73 (1993) 1377-1391
5. Mayas R.M., Maita H., and Staley J.P. Exon ligation is proofread by the DExD/H-box ATPase Prp22p. Nat Struct Mol Biol 13 (2006) 482-490. Using yeast spliceosomes stalled after the first step on a substrate with a mutated 3′-splice site, the authors provide evidence for an ATP-dependent mechanism that blocks the second step of splicing for mutant 3′-splice sites. Mutations of a spliceosomal helicase, Prp22, disable this mechanism, indicating a role for this helicase in splicing fidelity.
6. Query C.C., and Konarska M.M. Splicing fidelity revisited. Nat Struct Mol Biol 13 (2006) 472-474
7. Tsai R.T., Fu R.H., Yeh F.L., Tseng C.K., Lin Y.C., Huang Y.H., and Cheng S.C. Spliceosome disassembly catalyzed by Prp43 and its associated components Ntr1 and Ntr2. Genes Dev 19 (2005) 2991-3003
8. Pandit S., Lynn B., and Rymond B.C. Inhibition of a spliceosome turnover pathway suppresses splicing defects. Proc Natl Acad Sci USA 103 (2006) 13700-13705
9. Query C.C., and Konarska M.M. Suppression of multiple substrate mutations by spliceosomal prp8 alleles suggests functional correlations with ribosomal ambiguity mutants. Mol Cell 14 (2004) 343-354
10. Villa T., and Guthrie C. The Isy1p component of the NineTeen complex interacts with the ATPase Prp16p to regulate the fidelity of pre-mRNA splicing. Genes Dev 19 (2005) 1894-1904. In a screen for an extragenic suppressor of Prp16 in yeast, the authors find a single suppressor, a truncation mutant of ISY1. Deletion mutations of ISY1 led to a general increase in the fidelity of the first step and a more efficient second step with reduced fidelity.
11. Konarska M.M., and Query C.C. Insights into the mechanisms of splicing: more lessons from the ribosome. Genes Dev 19 (2005) 2255-2260
12. Konarska M.M., Vilardell J., and Query C.C. Repositioning of the reaction intermediate within the catalytic center of the spliceosome. Mol Cell 21 (2006) 543-553. Using a combination of genetic and biochemical analyses, the authors prove that mutations of non-conserved nucleotides of the 5′-splice site (positions +3 and +4) that increase complementarity to U6 result in a decrease in the efficiency of the second step of splicing. Mutations that reduce this complementarity lead to a general improvement in the efficiency of the second step.
13. Rhode B.M., Hartmuth K., Westhof E., and Luhrmann R. Proximity of conserved U6 and U2 snRNA elements to the 5′ splice site region in activated spliceosomes. EMBO J 25 (2006) 2475-2486. The authors probe the vicinity of the 5′-splice site by placing a site-tethered hydroxyl radical source at nucleotide +10 in human spliceosomes immediately before the first and second steps. Although the global pattern of cleavage of snRNAs and the pre-mRNA remains the same, there is a clear change in the cleavage pattern, consistent with a conformational rearrangement between the two steps.
14. Umen J.G., and Guthrie C. The second catalytic step of pre-mRNA splicing. RNA 1 (1995) 869-885
15. Small E.C., Leggett S.R., Winans A.A., and Staley J.P. The EF-G-like GTPase Snu114p regulates spliceosome dynamics mediated by Brr2p, a DExD/H box ATPase. Mol Cell 23 (2006) 389-399. Using purified yeast spliceosomes poised for disassembly, the authors prove a role for Snu114 and Brr2 in this step. Whereas adding GDP blocks disassembly, addition of GTP relieves this block. Using mutants that change the specificity of the GTP-binding domain of Snu114 to XTP, they prove that this effect is mediated by Snu114. In addition, the authors show an ATP-dependent role for Brr2 in spliceosome dissociation. Furthermore, both these proteins are involved in spliceosome activation, indicating a regulated function for these two remodeling factors in multiple steps of the spliceosomal cycle.
16. Bartels C., Urlaub H., Luhrmann R., and Fabrizio P. Mutagenesis suggests several roles of Snu114p in pre-mRNA splicing. J Biol Chem 278 (2003) 28324-28334
17. Brenner T.J., and Guthrie C. Genetic analysis reveals a role for the C terminus of the Saccharomyces cerevisiae GTPase Snu114 during spliceosome activation. Genetics 170 (2005) 1063-1080
18. Brenner T.J., and Guthrie C. Assembly of Snu114 into U5 snRNP requires Prp8 and a functional GTPase domain. RNA 12 (2006) 862-871
19. Bottner C.A., Schmidt H., Vogel S., Michele M., and Kaufer N.F. Multiple genetic and biochemical interactions of Brr2, Prp8, Prp31, Prp1 and Prp4 kinase suggest a function in the control of the activation of spliceosomes in Schizosaccharomyces pombe. Curr Genet 48 (2005) 151-161
20. Liu S., Rauhut R., Vornlocher H.P., and Luhrmann R. The network of protein-protein interactions within the human U4/U6.U5 tri-snRNP. RNA 12 (2006) 1418-1430. Using co-immunoprecipitation and yeast two-hybrid assays, the authors map the interactions between the various proteins found in human tri-snRNP. They elucidate a highly complex pattern of interactions between these proteins, which provides the basis for tri-snRNP stability and protein-protein interactions in the assembled spliceosome.
21. Boon K.L., Norman C.M., Grainger R.J., Newman A.J., and Beggs J.D. Prp8p dissection reveals domain structure and protein interaction sites. RNA 12 (2006) 198-205. A novel transposon-mediated approach is used by the authors to show that the highly conserved U5-specific protein Prp8 can be divided into two pieces at certain positions and that the two pieces are functional when both are provided in trans. In addition, the authors use the same approach to determine the regions of Prp8 that interact with Snu114 and Aar2.
22. Bellare P., Kutach A.K., Rines A.K., Guthrie C., and Sontheimer E.J. Ubiquitin binding by a variant Jab1/MPN domain in the essential pre-mRNA splicing factor Prp8p. RNA 12 (2006) 292-302
23. Valadkhan S., and Manley J.L. Splicing-related catalysis by protein-free snRNAs. Nature 413 (2001) 701-707
24. Grainger R.J., and Beggs J.D. Prp8 protein: at the heart of the spliceosome. RNA 11 (2005) 533-557
25. Turner I.A., Norman C.M., Churcher M.J., and Newman A.J. Dissection of Prp8 protein defines multiple interactions with crucial RNA sequences in the catalytic core of the spliceosome. RNA 12 (2006) 375-386. To map the regions of Prp8 that directly contact the spliceosomal snRNAs and the pre-mRNA, the authors use a novel transposon-mediated approach. Interestingly, the authors show that there are certain areas in Prp8 that tolerate the transposon insertions, whereas others do not. They also show that most protein-RNA interactions cluster in three regions in the central third of the protein.
26. Stark H., and Luhrmann R. Cryo-electron microscopy of spliceosomal components. Annu Rev Biophys Biomol Struct 35 (2006) 435-457
27. Sander B., Golas M.M., Makarov E.M., Brahms H., Kastner B., Luhrmann R., and Stark H. Organization of core spliceosomal components U5 snRNA loop I and U4/U6 di-snRNP within U4/U6.U5 tri-snRNP as revealed by electron cryomicroscopy. Mol Cell 24 (2006) 267-278. Purified human tri-snRNP, di-snRNP and U5 snRNP are subjected to cryo-EM analysis. Furthermore, the authors used a labeling approach to determine the site of conserved loop 1 and the tri-methylguanine cap of U5 snRNA in U5 snRNP and the tri-snRNP particle. The authors successfully fit the individual structures of U5 snRNP and di-snRNP into the deduced tri-snRNP structure.
28. Schellenberg M.J., Edwards R.A., Ritchie D.B., Kent O.A., Golas M.M., Stark H., Luhrmann R., Glover J.N., and MacMillan A.M. Crystal structure of a core spliceosomal protein interface. Proc Natl Acad Sci USA 103 (2006) 1266-1271
29. Spadaccini R., Reidt U., Dybkov O., Will C., Frank R., Stier G., Corsini L., Wahl M.C., Luhrmann R., and Sattler M. Biochemical and NMR analyses of an SF3b155-p14-U2AF-RNA interaction network involved in branch point definition during pre-mRNA splicing. RNA 12 (2006) 410-425
30. Deckert J., Hartmuth K., Boehringer D., Behzadnia N., Will C.L., Kastner B., Stark H., Urlaub H., and Luhrmann R. Protein composition and electron microscopy structure of affinity-purified human spliceosomal B complexes isolated under physiological conditions. Mol Cell Biol 26 (2006) 5528-5543
31. Jurica M.S., Sousa D., Moore M.J., and Grigorieff N. Three-dimensional structure of C complex spliceosomes by electron microscopy. Nat Struct Mol Biol 11 (2004) 265-269
32. Reyes J.L., Gustafson E.H., Luo H.R., Moore M.J., and Konarska M.M. The C-terminal region of hPrp8 interacts with the conserved GU dinucleotide at the 5′ splice site. RNA 5 (1999) 167-179
33. Perriman R.J., and Ares Jr. M. Rearrangement of competing U2 RNA helices within the spliceosome promotes multiple steps in splicing. Genes Dev 21 (2007) 811-820. Using yeast genetic analyses, the authors prove the presence a dynamic rearrangement in yeast U2 snRNA, in which a switch between the mutually exclusive stems IIa and IIc promotes different splicing steps.
34. Hilliker A.K., Mefford M.A., and Staley J.P. U2 toggles iteratively between the stem IIa and stem IIc conformations to promote pre-mRNA splicing. Genes Dev 21 (2007) 821-834. The authors show that U2 snRNA toggles between stem IIc, which seems to exist at the time of splicing catalysis, and stem IIa, which seems to promote the binding and release of substrates. The authors indicate that this switch is facilitated by Prp16.
35. Pena V., Liu S., Bujnicki J.M., Luhrmann R., and Wahl M.C. Structure of a multipartite protein-protein interaction domain in splicing factor prp8 and its link to retinitis pigmentosa. Mol Cell 25 (2007) 615-624. This work provides the first high-resolution structure of an hPrp8 fragment, proving the presence of a predicted Jab1/MPN domain. The authors also show that, in yeast two-hybrid assays, the mutations in the C terminus of hPrp8 that cause Retinitis pigmentosa diminish the interaction of Prp8 with hBrr2 and hSnu114 under stringent conditions.