Structural basis of branching during RNA splicing

Galej, W. P., Toor, N., Newman, A. J. & Nagai, K. Molecular mechanism and evolution of nuclear pre-mrna and group ii intron splicing: insights from cryo-electron microscopy structures. Chem. Rev. 118, 4156–4176 (2018).

Article  CAS  PubMed  Google Scholar 

Grabowski, P. J., Padgett, R. A. & Sharp, P. A. Messenger RNA splicing in vitro: an excised intervening sequence and a potential intermediate. Cell 37, 415–427 (1984).

Article  CAS  PubMed  Google Scholar 

Toor, N., Keating, K. S., Taylor, S. D. & Pyle, A. M. Crystal structure of a self-spliced group II intron. Science 320, 77–82 (2008).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Galej, W. P. et al. Cryo-EM structure of the spliceosome immediately after branching. Nature 537, 197–201 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hang, J., Wan, R., Yan, C. & Shi, Y. Structural basis of pre-mRNA splicing. Science 349, 1191–1198 (2015).

Article  CAS  PubMed  Google Scholar 

Padgett, R. A., Konarska, M. M., Grabowski, P. J., Hardy, S. F. & Sharp, P. A. Lariat RNA’s as intermediates and products in the splicing of messenger RNA precursors. Science 225, 898–903 (1984).

Article  CAS  PubMed  Google Scholar 

Konarska, M. M., Grabowski, P. J., Padgett, R. A. & Sharp, P. A. Characterization of the branch site in lariat RNAs produced by splicing of mRNA precursors. Nature 313, 552–557 (1985).

Article  CAS  PubMed  Google Scholar 

Peebles, C. L. et al. A self-splicing RNA excises an intron lariat. Cell 44, 213–223 (1986).

Article  CAS  PubMed  Google Scholar 

Robart, A. R., Chan, R. T., Peters, J. K., Rajashankar, K. R. & Toor, N. Crystal structure of a eukaryotic group II intron lariat. Nature 514, 193–197 (2014).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gao, K., Masuda, A., Matsuura, T. & Ohno, K. Human branch point consensus sequence is yUnAy. Nucleic Acids Res. 36, 2257–2267 (2008).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wan, R., Bai, R., Yan, C., Lei, J. & Shi, Y. Structures of the catalytically activated yeast spliceosome reveal the mechanism of branching. Cell 177, 339–351 (2019).

Article  CAS  PubMed  Google Scholar 

Wilkinson, M. E., Fica, S. M., Galej, W. P. & Nagai, K. Structural basis for conformational equilibrium of the catalytic spliceosome. Mol. Cell 81, 1439–1452 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jacquier, A. & Michel, F. Multiple exon-binding sites in class II self-splicing introns. Cell 50, 17–29 (1987).

Article  CAS  PubMed  Google Scholar 

Haack, D. B. et al. Cryo-EM structures of a group II intron reverse splicing into DNA. Cell 178, 612–623 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fedorova, O. & Pyle, A. M. Linking the group II intron catalytic domains: tertiary contacts and structural features of domain 3. EMBO J. 24, 3906–3916 (2005).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bertram, K. et al. Cryo-EM structure of a human spliceosome activated for step 2 of splicing. Nature 542, 318–323 (2017).

Article  CAS  PubMed  Google Scholar 

Fica, S. M., Mefford, M. A., Piccirilli, J. A. & Staley, J. P. Evidence for a group II intron-like catalytic triplex in the spliceosome. Nat. Struct. Mol. Biol. 21, 464–471 (2014).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fica, S. M. et al. RNA catalyses nuclear pre-mRNA splicing. Nature 503, 229–234 (2013).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Padgett, R. A., Podar, M., Boulanger, S. C. & Perlman, P. S. The stereochemical course of group II intron self-splicing. Science 266, 1685–1688 (1994).

Article  CAS  PubMed  Google Scholar 

Fica, S. M. et al. Structure of a spliceosome remodelled for exon ligation. Nature 542, 377–380 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Galej, W. P., Oubridge, C., Newman, A. J. & Nagai, K. Crystal structure of Prp8 reveals active site cavity of the spliceosome. Nature 493, 638–643 (2013).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Coimbatore Narayanan, B. et al. The Nucleic Acid Database: new features and capabilities. Nucleic Acids Res. 42, 114–122 (2014).

Article  Google Scholar 

Akiyama, B. M., Graham, M. E., O Donoghue, Z., Beckham, J. D. & Kieft, J. S. Three-dimensional structure of a flavivirus dumbbell RNA reveals molecular details of an RNA regulator of replication. Nucleic Acids Res. 49, 7122–7138 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mercer, T. R. et al. Genome-wide discovery of human splicing branchpoints. Genome Res. 25, 290–303 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chu, V. T., Adamidi, C., Liu, Q., Perlman, P. S. & Pyle, A. M. Control of branch-site choice by a group II intron. EMBO J. 20, 6866–6876 (2001).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Liu, Q. et al. Branch-site selection in a group II intron mediated by active recognition of the adenine amino group and steric exclusion of non-adenine functionalities. J. Mol. Biol. 267, 163–171 (1997).

Article  CAS  PubMed  Google Scholar 

Mitchell, D. et al. Glyoxals as in vivo RNA structural probes of guanine base-pairing. RNA 24, 114–124 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Taggart, A. J. et al. Large-scale analysis of branchpoint usage across species and cell lines. Genome Res 27, 639–649 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Carlomagno, T. et al. Structural principles of RNA catalysis in a 2′–5′ lariat-forming ribozyme. J. Am. Chem. Soc. 135, 4403–4411 (2013).

Article  CAS  PubMed  Google Scholar 

Sharp, P. A. ‘Five easy pieces’. Science 254, 663 (1991).

Article  CAS  PubMed  Google Scholar 

Database for bacterial group II introns. (2003) University of Calgary http://webapps2.ucalgary.ca/∼groupii/

Dai, L., Toor, N., Olson, R., Keeping, A. & Zimmerly, S. Database for mobile group II introns. Nucleic Acids Res. 31, 424–426 (2003).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tippmann, H. F. Analysis for free: comparing programs for sequence analysis. Brief. Bioinform. 5, 82–87 (2004).

Article  CAS  PubMed  Google Scholar 

Tan, Y. Z. et al. Addressing preferred specimen orientation in single-particle cryo-EM through tilting. Nat. Methods 14, 793–796 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Aiyer, S., Strutzenberg, T. S., Bowman, M. E., Noel, J. P. & Lyumkis, D. Single-particle cryo-EM data collection with stage tilt using Leginon. J. Vis. Exp. 185, e64136 (2022).

Google Scholar 

Suloway, C. et al. Automated molecular microscopy: the new Leginon system. J. Struct. Biol. 151, 41–60 (2005).

Article  CAS  PubMed  Google Scholar 

Cheng, A. et al. Leginon: new features and applications. Protein Sci. 30, 136–150 (2021).

Article  CAS  PubMed  Google Scholar 

Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).

Article 

留言 (0)

沒有登入
gif