Single molecule analysis reveals reversible and irreversible steps during spliceosome activation

eLife

Volumn 5, Issue MAY2016, 2016, Pages

  Hoskins, Aaron A ^a   Rodgers, Margaret L ^a   Friedman, Larry J ^b   Gelles, Jeff ^b   Moore, Melissa J ^c  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b BRANDEIS UNIVERSITY   (United States)

^c UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; SMALL NUCLEAR RIBONUCLEOPROTEIN; PRP19 PROTEIN, S CEREVISIAE; RNA PRECURSOR; RNA SPLICING FACTOR; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; FLUORESCENCE SPECTROSCOPY; GENE EXPRESSION; NONHUMAN; POLYACRYLAMIDE GEL ELECTROPHORESIS; SACCHAROMYCES CEREVISIAE; SPLICEOSOME; ENZYME ACTIVE SITE; GENETICS; METABOLISM; MOLECULAR DYNAMICS; RNA SPLICING; SINGLE MOLECULE IMAGING;

ADENOSINE TRIPHOSPHATE; CATALYTIC DOMAIN; MOLECULAR DYNAMICS SIMULATION; RIBONUCLEOPROTEIN, U4-U6 SMALL NUCLEAR; RNA PRECURSORS; RNA SPLICING; RNA SPLICING FACTORS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SINGLE MOLECULE IMAGING; SPLICEOSOMES;

EID: 84979516798     PISSN: None     EISSN: 2050084X     Source Type: Journal    
DOI: 10.7554/eLife.14166     Document Type: Article

References (55)

1. Abelson J, Blanco M, Ditzler MA, Fuller F, Aravamudhan P, Wood M, Villa T, Ryan DE, Pleiss JA, Maeder C, Guthrie C, Walter NG. 2010. Conformational dynamics of single pre-mRNA molecules during in vitro splicing. Nature Structural & Molecular Biology 17:504-512. doi: 10.1038/nsmb.1767
2. Anderson EG, Hoskins AA. 2014. Single molecule approaches for studying spliceosome assembly and catalysis. Methods in Molecular Biology 1126:217-241. doi: 10.1007/978-1-62703-980-2_17
3. Ansari A, Schwer B. 1995. SLU7 and a novel activity, SSF1, act during the PRP16-dependent step of yeast pre-mRNA splicing. The EMBO Journal 14:4001-4009.
4. Bellare P, Small EC, Huang X, Wohlschlegel JA, Staley JP, Sontheimer EJ. 2008. A role for ubiquitin in the spliceosome assembly pathway. Nature Structural & Molecular Biology 15:444-451. doi: 10.1038/nsmb.1401
5. Boesler C, Rigo N, Agafonov DE, Kastner B, Urlaub H, Will CL, Lührmann R. 2015. Stable tri-snRNP integration is accompanied by a major structural rearrangement of the spliceosome that is dependent on Prp8 interaction with the 5' splice site. RNA 21:1993-2005. doi: 10.1261/rna.053991.115
6. Brenner TJ, Guthrie C. 2006. Assembly of Snu114 into U5 snRNP requires Prp8 and a functional GTPase domain. RNA 12:862-871. doi: 10.1261/rna.2319806
7. Brow DA. 2002. Allosteric cascade of spliceosome activation. Annual Review of Genetics 36:333-360. doi: 10. 1146/annurev.genet.36.043002.091635
8. Burgess SM, Guthrie C. 1993. A mechanism to enhance mRNA splicing fidelity: the RNA-dependent ATPase Prp16 governs usage of a discard pathway for aberrant lariat intermediates. Cell 73:1377-1391. doi: 10.1016/0092-8674(93)90363-U
9. Burke JE, Butcher SE, Brow DA. 2015. Spliceosome assembly in the absence of stable U4/U6 RNA pairing. RNA 21:923-934. doi: 10.1261/rna.048421.114
10. Chan SP, Kao DI, Tsai WY, Cheng SC. 2003. The Prp19p-associated complex in spliceosome activation. Science 302:279-282. doi: 10.1126/science.1086602
11. Chen C, Greenberg MJ, Laakso JM, Ostap EM, Goldman YE, Shuman H. 2012. Kinetic schemes for post-synchronized single molecule dynamics. Biophysical Journal 102:L23-25. doi: 10.1016/j.bpj.2012.01.054
12. Cheng SC, Abelson J. 1987. Spliceosome assembly in yeast. Genes & Development 1:1014-1027. doi: 10.1101/gad.1.9.1014
13. Cherny D, Gooding C, Eperon GE, Coelho MB, Bagshaw CR, Smith CW, Eperon IC. 2010. Stoichiometry of a regulatory splicing complex revealed by single-molecule analyses. The EMBO Journal 29:2161-2172. doi: 10. 1038/emboj.2010.103
14. Chiou NT, Shankarling G, Lynch KW. 2013. hnRNP L and hnRNP A1 induce extended U1 snRNA interactions with an exon to repress spliceosome assembly. Molecular Cell 49:972-982. doi: 10.1016/j.molcel.2012.12.025
15. Colquhoun D, Hawkes AG. 1995. The Principles of Stochastic Interpretation of Ion-Channel Mechanisms. In:Sakmann B, Neher E (Eds). Single-Channel Recording (2nd ed). New York: Plenum Press. doi: 10.1007/978-1-4419-1229-9_18
16. Crawford DJ, Hoskins AA, Friedman LJ, Gelles J, Moore MJ. 2008. Visualizing the splicing of single pre-mRNA molecules in whole cell extract. RNA 14:170-179. doi: 10.1261/rna.794808
17. Crawford DJ, Hoskins AA, Friedman LJ, Gelles J, Moore MJ. 2013. Single-molecule colocalization FRET evidence that spliceosome activation precedes stable approach of 5' splice site and branch site. Proceedings of the National Academy of Sciences of the United States of America 110:6783-6788. doi: 10.1073/pnas.1219305110
18. de Almeida RA, O’Keefe RT. 2015. The NineTeen Complex (NTC) and NTC-associated proteins as targets for spliceosomal ATPase action during pre-mRNA splicing. RNA Biology 12:109-114. doi: 10.1080/15476286.2015. 1008926
19. Fabrizio P, Dannenberg J, Dube P, Kastner B, Stark H, Urlaub H, Lührmann R. 2009. The evolutionarily conserved core design of the catalytic activation step of the yeast spliceosome. Molecular Cell 36:593-608. doi: 10.1016/j.molcel.2009.09.040
20. Fabrizio P, McPheeters DS, Abelson J. 1989. In vitro assembly of yeast U6 snRNP: a functional assay. Genes & Development 3:2137-2150. doi: 10.1101/gad.3.12b.2137
21. Friedman LJ, Chung J, Gelles J. 2006. Viewing dynamic assembly of molecular complexes by multi-wavelength single-molecule fluorescence. Biophysical Journal 91:1023-1031. doi: 10.1529/biophysj.106.084004
22. Guo Z, Karunatilaka KS, Rueda D. 2009. Single-molecule analysis of protein-free U2-U6 snRNAs. Nature Structural & Molecular Biology 16:1154-1159. doi: 10.1038/nsmb.1672
23. Hardin JW, Warnasooriya C, Kondo Y, Nagai K, Rueda D. 2015. Assembly and dynamics of the U4/U6 di-snRNP by single-molecule FRET. Nucleic Acids Research 43:10963-10974. doi: 10.1093/nar/gkv1011
24. Held P. 2010. Monitoring Growth of Beer Brewing Strains of Saccharomyces Cerevisiae. Application Note.BioTek. http://www.biotek.com/resources/articles/beer-brewing-synergyh1-yeast-growth.html.
25. Hogg R, McGrail JC, O’Keefe RT. 2010. The function of the NineTeen Complex (NTC) in regulating spliceosome conformations and fidelity during pre-mRNA splicing. Biochemical Society Transactions 38:1110-1115. doi: 10. 1042/BST0381110
26. Hoskins AA, Friedman LJ, Gallagher SS, Crawford DJ, Anderson EG, Wombacher R, Ramirez N, Cornish VW, Gelles J, Moore MJ. 2011. Ordered and dynamic assembly of single spliceosomes. Science 331:1289-1295. doi: 10.1126/science.1198830
27. Hoskins AA, Moore MJ. 2012. The spliceosome: a flexible, reversible macromolecular machine. Trends in Biochemical Sciences 37:179-188. doi: 10.1016/j.tibs.2012.02.009
28. Huang YH, Chung CS, Kao DI, Kao TC, Cheng SC. 2014. Sad1 counteracts Brr2-mediated dissociation of U4/U6. U5 in tri-snRNP homeostasis. Molecular and Cellular Biology 34:210-220. doi: 10.1128/MCB.00837-13
29. Karunatilaka KS, Rueda D. 2014. Post-transcriptional modifications modulate conformational dynamics in human U2-U6 snRNA complex. RNA 20:16-23. doi: 10.1261/rna.041806.113
30. Konarska MM, Sharp PA. 1986. Electrophoretic separation of complexes involved in the splicing of precursors to mRNAs. Cell 46:845-855. doi: 10.1016/0092-8674(86)90066-8
31. Koodathingal P, Novak T, Piccirilli JA, Staley JP. 2010. The DEAH box ATPases Prp16 and Prp43 cooperate to proofread 5' splice site cleavage during pre-mRNA splicing. Molecular Cell 39:385-395. doi: 10.1016/j.molcel. 2010.07.014
32. Krishnan R, Blanco MR, Kahlscheuer ML, Abelson J, Guthrie C, Walter NG. 2013. Biased Brownian ratcheting leads to pre-mRNA remodeling and capture prior to first-step splicing. Nature Structural & Molecular Biology 20:1450-1457. doi: 10.1038/nsmb.2704
33. Lardelli RM, Thompson JX, Yates JR, Stevens SW. 2010. Release of SF3 from the intron branchpoint activates the first step of pre-mRNA splicing. RNA 16:516-528. doi: 10.1261/rna.2030510
34. Larson JD, Rodgers ML, Hoskins AA. 2014. Visualizing cellular machines with colocalization single molecule microscopy. Chemical Society Review 43:1189-1200. doi: 10.1039/C3CS60208G
35. Legrain P, Seraphin B, Rosbash M. 1988. Early commitment of yeast pre-mRNA to the spliceosome pathway. Molecular and Cellular Biology 8:3755-3760. doi: 10.1128/MCB.8.9.3755
36. Liu H-L, Cheng S-C. 2012. The Interaction of Prp2 with a Defined Region of the Intron Is Required for the First Splicing Reaction. Molecular and Cellular Biology 32:5056-5066. doi: 10.1128/MCB.01109-12
37. Lu HP, Xun L, Xie XS. 1998. Single-molecule enzymatic dynamics. Science 282:1877-1882. doi: 10.1126/science. 282.5395.1877
38. Mayas RM, Maita H, Staley JP. 2006. Exon ligation is proofread by the DExD/H-box ATPase Prp22p. Nature Structural & Molecular Biology 13:482-490. doi: 10.1038/nsmb1093
39. Raghunathan PL, Guthrie C. 1998a. A spliceosomal recycling factor that reanneals U4 and U6 small nuclear ribonucleoprotein particles. Science 279:857-860. doi: 10.1126/science.279.5352.857
40. Raghunathan PL, Guthrie C. 1998b. RNA unwinding in U4/U6 snRNPs requires ATP hydrolysis and the DEIH-box splicing factor Brr2. Current Biology 8:847-855. doi: 10.1016/S0960-9822(07)00345-4
41. Rasche N, Dybkov O, Schmitzová J, Akyildiz B, Fabrizio P, Lührmann R. 2012. Cwc2 and its human homologue RBM22 promote an active conformation of the spliceosome catalytic centre. The EMBO Journal 31:1591-1604. doi: 10.1038/emboj.2011.502
42. Rodgers ML, Paulson J, Hoskins AA. 2015. Rapid isolation and single-molecule analysis of ribonucleoproteins from cell lysate by SNAP-SiMPull. RNA 21:1031-1041. doi: 10.1261/rna.047845.114
43. Ruby SW, Abelson J. 1988. An early hierarchic role of U1 small nuclear ribonucleoprotein in spliceosome assembly. Science 242:1028-1035. doi: 10.1126/science.2973660
44. Shcherbakova I, Hoskins AA, Friedman LJ, Serebrov V, Corrêa IR, Xu MQ, Gelles J, Moore MJ. 2013. Alternative spliceosome assembly pathways revealed by single-molecule fluorescence microscopy. Cell Reports 5:151-165. doi: 10.1016/j.celrep.2013.08.026
45. Small EC, Leggett SR, Winans AA, Staley JP. 2006. The EF-G-like GTPase Snu114p regulates spliceosome dynamics mediated by Brr2p, a DExD/H box ATPase. Molecular Cell 23:389-399. doi: 10.1016/j.molcel.2006. 05.043
46. Staley JP, Guthrie C. 1999. An RNA switch at the 5' splice site requires ATP and the DEAD box protein Prp28p. Molecular Cell 3:55-64. doi: 10.1016/S1097-2765(00)80174-4
47. Sun X, Zhang A, Baker B, Sun L, Howard A, Buswell J, Maurel D, Masharina A, Johnsson K, Noren CJ, Xu M-Q, Corrêa IR. 2011. Development of SNAP-Tag Fluorogenic Probes for Wash-Free Fluorescence Imaging. ChemBioChem 12:2217-2226. doi: 10.1002/cbic.201100173
48. Tardiff DF, Rosbash M. 2006. Arrested yeast splicing complexes indicate stepwise snRNP recruitment during in vivo spliceosome assembly. RNA 12:968-979. doi: 10.1261/rna.50506
49. Tarn WY, Lee KR, Cheng SC. 1993. Yeast precursor mRNA processing protein PRP19 associates with the spliceosome concomitant with or just after dissociation of U4 small nuclear RNA. Proceedings of the National Academy of Sciences of the United States of America 90:10821-10825. doi: 10.1073/pnas.90.22.10821
50. Tseng CK, Cheng SC. 2008. Both catalytic steps of nuclear pre-mRNA splicing are reversible. Science 320:1782-1784. doi: 10.1126/science.1158993
51. Wahl MC, Will CL, Lührmann R. 2009. The spliceosome: design principles of a dynamic RNP machine. Cell 136:701-718. doi: 10.1016/j.cell.2009.02.009
52. Walter NG, Huang CY, Manzo AJ, Sobhy MA. 2008. Do-it-yourself guide: how to use the modern single-molecule toolkit. Nature Methods 5:475-489. doi: 10.1038/nmeth.1215
53. Wlodaver AM, Staley JP. 2014. The DExD/H-box ATPase Prp2p destabilizes and proofreads the catalytic RNA core of the spliceosome. RNA 20:282-294. doi: 10.1261/rna.042598.113
54. Yan C, Hang J, Wan R, Huang M, Wong CC, Shi Y. 2015. Structure of a yeast spliceosome at 3.6-angstrom resolution. Science 349:1182-1191. doi: 10.1126/science.aac7629
55. Yang F, Wang XY, Zhang ZM, Pu J, Fan YJ, Zhou J, Query CC, Xu YZ. 2013. Splicing proofreading at 5' splice sites by ATPase Prp28p. Nucleic Acids Research 41:4660-4670. doi: 10.1093/nar/gkt149