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Structures of the Catalytically Activated Yeast Spliceosome Reveal the Mechanism of Branching.

Wan R, Bai R, Yan C, Lei J, Shi Y
Cell 177 339-351.e13 (2019)
Related entries: 6j6g, 6j6h, 6j6q

Cited: 40 times
EuropePMC logo PMID: 30879786

Abstract

Pre-mRNA splicing is executed by the spliceosome. Structural characterization of the catalytically activated complex (B∗) is pivotal for understanding the branching reaction. In this study, we assembled the B∗ complexes on two different pre-mRNAs from Saccharomyces cerevisiae and determined the cryo-EM structures of four distinct B∗ complexes at overall resolutions of 2.9-3.8 Å. The duplex between U2 small nuclear RNA (snRNA) and the branch point sequence (BPS) is discretely away from the 5'-splice site (5'SS) in the three B∗ complexes that are devoid of the step I splicing factors Yju2 and Cwc25. Recruitment of Yju2 into the active site brings the U2/BPS duplex into the vicinity of 5'SS, with the BPS nucleophile positioned 4 Å away from the catalytic metal M2. This analysis reveals the functional mechanism of Yju2 and Cwc25 in branching. These structures on different pre-mRNAs reveal substrate-specific conformations of the spliceosome in a major functional state.

Reviews citing this publication (8)

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Articles citing this publication (32)

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  5. m6A modification of U6 snRNA modulates usage of two major classes of pre-mRNA 5' splice site. Parker MT, Soanes BK, Kusakina J, Larrieu A, Knop K, Joy N, Breidenbach F, Sherwood AV, Barton GJ, Fica SM, Davies BH, Simpson GG. Elife 11 e78808 (2022)
  6. Termination of pre-mRNA splicing requires that the ATPase and RNA unwindase Prp43p acts on the catalytic snRNA U6. Toroney R, Nielsen KH, Staley JP. Genes Dev 33 1555-1574 (2019)
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  10. Monovalent metal ion binding promotes the first transesterification reaction in the spliceosome. Aupič J, Borišek J, Fica SM, Galej WP, Magistrato A. Nat Commun 14 8482 (2023)
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  12. A molecular brake that modulates spliceosome pausing at detained introns contributes to neurodegeneration. Meng D, Zheng Q, Zhang X, Piao X, Luo L, Jia Y. Protein Cell 14 318-336 (2023)
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  14. Inter-species association mapping links splice site evolution to METTL16 and SNRNP27K. Parker MT, Fica SM, Barton GJ, Simpson GG. Elife 12 e91997 (2023)
  15. Detecting circRNA in purified spliceosomal P complex. Shi S, Li X, Zhao R. Methods 196 30-35 (2021)
  16. Network theory reveals principles of spliceosome structure and dynamics. Kaur H, van der Feltz C, Sun Y, Hoskins AA. Structure 30 190-200.e2 (2022)
  17. Role of the central junction in folding topology of the protein-free human U2-U6 snRNA complex. Chu H, Perea W, Greenbaum NL. RNA 26 836-850 (2020)
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  19. A Mechanism Leading to Changes in Copy Number Variations Affected by Transcriptional Level Might Be Involved in Evolution, Embryonic Development, Senescence, and Oncogenesis Mediated by Retrotransposons. Sui Y, Peng S. Front Cell Dev Biol 9 618113 (2021)
  20. Biochemical and genetic evidence supports Fyv6 as a second-step splicing factor in Saccharomyces cerevisiae. Lipinski KA, Senn KA, Zeps NJ, Hoskins AA. RNA 29 1792-1802 (2023)
  21. A Snu114-GTP-Prp8 module forms a relay station for efficient splicing in yeast. Jia J, Ganichkin OM, Preußner M, Absmeier E, Alings C, Loll B, Heyd F, Wahl MC. Nucleic Acids Res 48 4572-4584 (2020)
  22. Altered splicing factor and alternative splicing events in a mouse model of diet- and polychlorinated biphenyl-induced liver disease. Petri BJ, Piell KM, Wahlang B, Head KZ, Rouchka EC, Park JW, Hwang JY, Banerjee M, Cave MC, Klinge CM. Environ Toxicol Pharmacol 103 104260 (2023)
  23. Functional analysis of Cwc24 ZF-domain in 5' splice site selection. Wu NY, Cheng SC. Nucleic Acids Res 47 10327-10339 (2019)
  24. Topology of the U12-U6atac snRNA Complex of the Minor Spliceosome and Binding by NTC-Related Protein RBM22. Ciavarella J, Perea W, Greenbaum NL. ACS Omega 5 23549-23558 (2020)
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  27. Missplicing suppressor alleles of Arabidopsis PRE-MRNA PROCESSING FACTOR 8 increase splicing fidelity by reducing the use of novel splice sites. Cabezas-Fuster A, Micol-Ponce R, Fontcuberta-Cervera S, Ponce MR. Nucleic Acids Res 50 5513-5527 (2022)
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  29. Phylogeny and conservation of plant U2A/U2A', a core splicing component in U2 spliceosomal complex. Liu Y, Tian Y, Wang LX, Fan T, Zhang J, Chen MX, Liu YG. Planta 255 25 (2021)
  30. Truncating the spliceosomal 'rope protein' Prp45 results in Htz1 dependent phenotypes. Abrhámová K, Groušlová M, Valentová A, Hao X, Liu B, Převorovský M, Gahura O, Půta F, Sunnerhagen P, Folk P. RNA Biol 21 1-17 (2024)
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  32. Variation of C-terminal domain governs RNA polymerase II genomic locations and alternative splicing in eukaryotic transcription. Zhang Q, Kim W, Panina SB, Mayfield JE, Portz B, Zhang YJ. Nat Commun 15 7985 (2024)


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