Dynamic Contacts of U2, RES, Cwc25, Prp8 and Prp45 Proteins with the Pre-mRNA Branch-Site and 3' Splice Site during Catalytic Activation and Step 1 Catalysis in Yeast Spliceosomes

English version České info

The spliceosome is a highly dynamic RNP machine that during the catalytic cycle undergoes many changes in composition and conformation. The pre-catalytic Bact spliceosome contains the U2, U6 and U5 snRNAs and ~40 proteins, which are evolutionarily conserved between budding yeast and metazoans. The Bact spliceosome is converted to a catalytically-activated B* spliceosome and following recruitment of the Cwc25 protein, step 1 of splicing is catalyzed and the C spliceosome is generated. The U2 snRNP plays an essential role in branch-site selection and pre-mRNA splicing catalysis. During the Bact to B* transition the affinity of several U2 SF3a/b proteins for the spliceosome is significantly reduced. Whether this is due to remodeling events affecting U2 snRNP contacts with the pre-mRNA is not known. Information about conserved spliceosomal protein-pre-mRNA contacts and their dynamics during splicing remains limited. Here we investigated pre-mRNA–protein contact sites in yeast Bact spliceosomes by UV-induced crosslinking. We detected contacts of nucleotides surrounding the branch-site with several of the U2 SF3a/b proteins, and we show that these interactions are evolutionarily conserved. We carried out a similar investigation with B* and C spliceosomes and provide important insights into the dynamics of pre-mRNA–protein interactions involving the essential U2, RES, Cwc25, Prp8 and Prp45 proteins.

Vyšlo v časopise: Dynamic Contacts of U2, RES, Cwc25, Prp8 and Prp45 Proteins with the Pre-mRNA Branch-Site and 3' Splice Site during Catalytic Activation and Step 1 Catalysis in Yeast Spliceosomes. PLoS Genet 11(9): e32767. doi:10.1371/journal.pgen.1005539
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1005539

Souhrn

Zdroje

1. Will CL, Lührmann R Spliceosome structure and function. Cold Spring Harb Perspect Biol 2011;3 : 1–23.

2. Wahl MC, Will CL, Lührmann R The spliceosome: design principles of a dynamic RNP machine. Cell 2009;136 : 701–718. doi: 10.1016/j.cell.2009.02.009 19239890

3. Staley JP, Guthrie C Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell 1998;92 : 315–326. 9476892

4. Nilsen TW RNA-RNA interactions in the spliceosome: unraveling the ties that bind. Cell 1994;78 : 1–4. 7518355

5. Fabrizio P, Dannenberg J, Dube P, Kastner B, Stark H, et al. The evolutionarily conserved core design of the catalytic activation step of the yeast spliceosome. Mol Cell 2009;36 : 593–608. doi: 10.1016/j.molcel.2009.09.040 19941820

6. Kim SH, Lin RJ Spliceosome activation by PRP2 ATPase prior to the first transesterification reaction of pre-mRNA splicing. Mol Cell Biol 1996;16 : 6810–6819. 8943336

7. Warkocki Z, Odenwälder P, Schmitzová J, Platzmann F, Stark H, et al. Reconstitution of both steps of Saccharomyces cerevisiae splicing with purified spliceosomal components. Nat Struct Mol Biol 2009;16 : 1237–1243. doi: 10.1038/nsmb.1729 19935684

8. Warkocki Z, Schneider C, Mozaffari-Jovin S, Schmitzová J, Hobartner C, et al. The G-patch protein Spp2 couples the spliceosome-stimulated ATPase activity of the DEAH-box protein Prp2 to catalytic activation of the spliceosome. Genes Dev 2015;29 : 94–107. doi: 10.1101/gad.253070.114 25561498

9. Chiu YF, Liu YC, Chiang TW, Yeh TC, Tseng CK, et al. Cwc25 is a novel splicing factor required after Prp2 and Yju2 to facilitate the first catalytic reaction. Mol Cell Biol 2009;29 : 5671–5678. doi: 10.1128/MCB.00773-09 19704000

10. Dziembowski A, Ventura AP, Rutz B, Caspary F, Faux C, et al. Proteomic analysis identifies a new complex required for nuclear pre-mRNA retention and splicing. EMBO J 2004;23 : 4847–4856. 15565172

11. Ohrt T, Prior M, Dannenberg J, Odenwälder P, Dybkov O, et al. Prp2-mediated protein rearrangements at the catalytic core of the spliceosome as revealed by dcFCCS. RNA 2012;18 : 1244–1256. doi: 10.1261/rna.033316.112 22535589

12. Lardelli RM, Thompson JX, Yates JR 3rd, Stevens SW Release of SF3 from the intron branchpoint activates the first step of pre-mRNA splicing. RNA 2010;16 : 516–528. doi: 10.1261/rna.2030510 20089683

13. Query CC, Moore MJ, Sharp PA Branch nucleophile selection in pre-mRNA splicing: evidence for the bulged duplex model. Genes Dev 1994;8 : 587–597. 7926752

14. Gozani O, Potashkin J, Reed R A potential role for U2AF-SAP 155 interactions in recruiting U2 snRNP to the branch site. Mol Cell Biol 1998;18 : 4752–4760. 9671485

15. Gozani O, Feld R, Reed R Evidence that sequence-independent binding of highly conserved U2 snRNP proteins upstream of the branch site is required for assembly of spliceosomal complex A. Genes Dev 1996;10 : 233–243. 8566756

16. Hodges PE, Beggs JD RNA splicing. U2 fulfils a commitment. Curr Biol 1994;4 : 264–267. 7922333

17. Krämer A The structure and function of proteins involved in mammalian pre-mRNA splicing. Annu Rev Biochem 1996;65 : 367–409. 8811184

18. Wang Q, He J, Lynn B, Rymond BC Interactions of the yeast SF3b splicing factor. Mol Cell Biol 2005;25 : 10745–10754. 16314500

19. McPheeters DS, Muhlenkamp P Spatial organization of protein-RNA interactions in the branch site-3' splice site region during pre-mRNA splicing in yeast. Mol Cell Biol 2003;23 : 4174–4186. 12773561

20. Wysoczanski P, Schneider C, Xiang S, Munari F, Trowitzsch S, et al. Cooperative structure of the heterotrimeric pre-mRNA retention and splicing complex. Nat Struct Mol Biol 2014;21 : 911–918. doi: 10.1038/nsmb.2889 25218446

21. Breaker RR, Joyce GF A DNA enzyme that cleaves RNA. Chem Biol 1994;1 : 223–229. 9383394

22. Moore MJ, Sharp PA Site-specific modification of pre-mRNA: the 2'-hydroxyl groups at the splice sites. Science 1992;256 : 992–997. 1589782

23. Agafonov DE, Deckert J, Wolf E, Odenwälder P, Bessonov S, et al. Semiquantitative Proteomic Analysis of the Human Spliceosome via a Novel Two-Dimensional Gel Electrophoresis Method. Mol Cell Biol 2011;31 : 2667–2682. doi: 10.1128/MCB.05266-11 21536652

24. Fourmann JB, Schmitzová J, Christian H, Urlaub H, Ficner R, et al. Dissection of the factor requirements for spliceosome disassembly and the elucidation of its dissociation products using a purified splicing system. Genes Dev 2013;27 : 413–428. doi: 10.1101/gad.207779.112 23431055

25. Silverman SK, Baum DA Use of deoxyribozymes in RNA research. Methods Enzymol 2009;469 : 95–117. doi: 10.1016/S0076-6879(09)69005-4 20946786

26. Cameron V, Uhlenbeck OC 3'-Phosphatase activity in T4 polynucleotide kinase. Biochemistry 1977;16 : 5120–5126. 199248

27. van Roon AM, Loening NM, Obayashi E, Yang JC, Newman AJ, et al. Solution structure of the U2 snRNP protein Rds3p reveals a knotted zinc-finger motif. Proc Natl Acad Sci U S A 2008;105 : 9621–9626. doi: 10.1073/pnas.0802494105 18621724

28. Teigelkamp S, Newman AJ, Beggs JD Extensive interactions of PRP8 protein with the 5' and 3' splice sites during splicing suggest a role in stabilization of exon alignment by U5 snRNA. EMBO J 1995;14 : 2602–2612. 7781612

29. Teigelkamp S, Whittaker E, Beggs JD Interaction of the yeast splicing factor PRP8 with substrate RNA during both steps of splicing. Nucleic Acids Res 1995;23 : 320–326. 7885825

30. Umen JG, Guthrie C A novel role for a U5 snRNP protein in 3' splice site selection. Genes Dev 1995;9 : 855–868. 7535718

31. Umen JG, Guthrie C Prp16p, Slu7p, and Prp8p interact with the 3' splice site in two distinct stages during the second catalytic step of pre-mRNA splicing. RNA 1995;1 : 584–597. 7489518

32. Chen HC, Tseng CK, Tsai RT, Chung CS, Cheng SC Link of NTR-mediated spliceosome disassembly with DEAH-box ATPases Prp2, Prp16, and Prp22. Mol Cell Biol 2013;33 : 514–525. doi: 10.1128/MCB.01093-12 23166295

33. Albers M, Diment A, Muraru M, Russell CS, Beggs JD Identification and characterization of Prp45p and Prp46p, essential pre-mRNA splicing factors. RNA 2003;9 : 138–150. 12554883

34. Staknis D, Reed R Direct interactions between pre-mRNA and six U2 small nuclear ribonucleoproteins during spliceosome assembly. Mol Cell Biol 1994;14 : 2994–3005. 8164655

35. Gozani O, Patton JG, Reed R A novel set of spliceosome-associated proteins and the essential splicing factor PSF bind stably to pre-mRNA prior to catalytic step II of the splicing reaction. EMBO J 1994;13 : 3356–3367. 8045264

36. Zhou Y, Chen C, Johansson MJ The pre-mRNA retention and splicing complex controls tRNA maturation by promoting TAN1 expression. Nucleic Acids Res 2013;41 : 5669–5678. doi: 10.1093/nar/gkt269 23605039

37. Tripsianes K, Friberg A, Barrandon C, Brooks M, van Tilbeurgh H, et al. A novel protein-protein interaction in the RES (REtention and Splicing) complex. J Biol Chem 2014;289 : 28640–28650. doi: 10.1074/jbc.M114.592311 25160624

38. Trowitzsch S, Weber G, Luhrmann R, Wahl MC Crystal structure of the Pml1p subunit of the yeast precursor mRNA retention and splicing complex. J Mol Biol 2009;385 : 531–541. doi: 10.1016/j.jmb.2008.10.087 19010333

39. Trowitzsch S, Weber G, Luhrmann R, Wahl MC An unusual RNA recognition motif acts as a scaffold for multiple proteins in the pre-mRNA retention and splicing complex. J Biol Chem 2008;283 : 32317–32327. doi: 10.1074/jbc.M804977200 18809678

40. Brooks MA, Dziembowski A, Quevillon-Cheruel S, Henriot V, Faux C, et al. Structure of the yeast Pml1 splicing factor and its integration into the RES complex. Nucleic Acids Res 2009;37 : 129–143. doi: 10.1093/nar/gkn894 19033360

41. Gottschalk A, Bartels C, Neubauer G, Lührmann R, Fabrizio P A Novel Yeast U2 snRNP Protein, Snu17p, Is Required for the First Catalytic Step of Splicing and for Progression of Spliceosome Assembly. Mol Cell Biol 2001;21 : 3037–3046. 11287609

42. Liu HL, Cheng SC The interaction of Prp2 with a defined region of the intron is required for the first splicing reaction. Mol Cell Biol 2012;32 : 5056–5066. doi: 10.1128/MCB.01109-12 23071087

43. Wlodaver AM, Staley JP The DExD/H-box ATPase Prp2p destabilizes and proofreads the catalytic RNA core of the spliceosome. RNA 2014;20 : 282–294. doi: 10.1261/rna.042598.113 24442613

44. Grainger RJ, Beggs JD Prp8 protein: at the heart of the spliceosome. RNA 2005;11 : 533–557. 15840809

45. Umen JG, Guthrie C The second catalytic step of pre-mRNA splicing. RNA 1995;1 : 869–885. 8548652

46. Coelho Ribeiro Mde L, Espinosa J, Islam S, Martinez O, Thanki JJ, et al. Malleable ribonucleoprotein machine: protein intrinsic disorder in the Saccharomyces cerevisiae spliceosome. PeerJ 2013;1: e2. doi: 10.7717/peerj.2 23638354

47. Gahura O, Abrhamova K, Skruzny M, Valentova A, Munzarova V, et al. Prp45 affects Prp22 partition in spliceosomal complexes and splicing efficiency of non-consensus substrates. J Cell Biochem 2009;106 : 139–151. doi: 10.1002/jcb.21989 19016306

48. McPheeters DS, Schwer B, Muhlenkamp P Interaction of the yeast DExH-box RNA helicase prp22p with the 3' splice site during the second step of nuclear pre-mRNA splicing. Nucleic Acids Res 2000;28 : 1313–1321. 10684925