Sculpting of the spliceosomal branch site recognition motif by a conserved pseudouridine

Nature Structural Biology

Volumn 9, Issue 12, 2002, Pages 958-965

  Newby, Meredith I ^a   Greenbaum, Nancy L ^a  

^a FLORIDA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE; DNA BASE; MESSENGER RNA PRECURSOR; SMALL NUCLEAR RNA;

ARTICLE; CONSENSUS SEQUENCE; MOLECULAR RECOGNITION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN MOTIF; RNA SPLICING; SACCHAROMYCES CEREVISIAE; SPLICEOSOME;

ADENOSINE; BASE SEQUENCE; BINDING SITES; INTRONS; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; PHYLOGENY; PSEUDOURIDINE; RNA PRECURSORS; RNA SPLICING; RNA, FUNGAL; SACCHAROMYCES CEREVISIAE; SPLICEOSOMES; URIDINE;

EUKARYOTA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0036896469     PISSN: 10728368     EISSN: None     Source Type: Journal    
DOI: 10.1038/nsb873     Document Type: Article

References (47)

1. Moore, M., Query, C. & Sharp, R in The RNA World (eds Gesteland, R.F. & Atkins, J.F.) 303-357 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor; 1993).
2. Madhani, H.D. & Guthrie, C. A novel base-pairing interaction between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome, Annu. Rev. Genet. 28, 1-26 (1994).
3. Valadkhan, S. & Manley, J.L. Splicing-related catalysis by protein-free snRNAs. Nature 413, 701-707 (2001).
4. Lane, B.G. in Modification and Editing of RNA (eds Grosjean, H. & Benne, R.) 1-20 (ASM Press, Washington, D.C.; 1998).
5. Yu, Y.-T., Shu, M.-D. & Steitz, J.A. Modification of U2 snRNA are required for snRNP assembly and pre-mRNA splicing. EMBO J. 17, 5783-5795 (1998).
6. Reddy, R. & Busch, H. in Structure and Function of Major and Minor Small Nuclear Ribonucleoprotein Particles (ed. Birnstiel, M.L.) 1-37 (Springer-Verlag Press, Berlin; 1988).
7. Patton, J., Jacobsen, M. & Pederson, T. Pseudouridine formation in small nuclear RNA. Proc. Natl. Acad. Sci. USA 91, 3324-3328 (1994).
8. Gu, J., Patton, J., Shimba, S. & Reddy, R. Localization of modified nucleotides in Schizosaccharomyces pombe spliceosomal small nuclear RNAs: Modified nucleotides are clustered in functionally important regions. RNA 2, 909-918 (1996).
9. Massenet, S. et al. Pseudouridine mapping in spliuceosomal U snRNAs (snRNAs) reveals that pseudouridine synthase pus1p exhibits a dual substrate specificity for U2 snRNA and tRNA. Mol. Cell. Biol. 19, 2142-2154 (1999).
10. McPheeters, D.S. & Abelson, J. Mutational analysis of the yeast U2 snRNA suggests a structural similarity to the catalytic core of group I introns. Cell 71, 819-831 (1992).
11. Pascolo, E. & Seraphin, B. The branchpoint residue is recognized during commitment complex formation before being bulged out of the U2 snRNA-pre-mRNA duplex. Mol. Cell. Biol. 17, 3469-3476 (1997).
12. Wu, J. & Manley, J.L. Mammalian pre-mRNA branch site selection by U2 snRNP involves base-pairing. Genes Dev. 3, 1553-1561 (1989).
13. Newby, M.I. & Greenbaum, N.L. A conserved pseudouridine modification in eukaryotic U2 snRNA induces a change in branch site architecture. RNA 7, 833-845 (2001).
14. Zagorowska, I. & Adamiak, R.W. 2-Aminopurine labeled RNA bulge loops. Synthesis and thermodynamics. Biochimie 78, 123-130 (1996).
15. Rachofsky, E.L., Osman, R. & Ross, J.B.A. Probing structure and dynamics of DNA with 2-aminopurine. Biochemistry 40, 946-956 (2001).
16. Kulinski, T. et al. Introductory data on dynamics of RNA bulge duplexes, 2-aminopurine labeled adenosine loops. Collect. Czech. Chem. Commun. 61, S265-S267 (1996).
17. Smith, J.S. & Nikonowicz, E.P. NMR structure and dynamics of an RNA motif common to the spliceosome branch-point helix and the RNA-binding site for phage GA coat protein. Biochemistry 37, 13486-13498.
18. Jucker, F.M. Heus, H.A., Yip, P.F., Moors, E.H.M. & Pardi, A. A network of heterogeneous hydrogen bonds in GNRA tetraloops. J. Mol. Biol. 264, 968-980 (1996).
19. Nissen, R. Ippolito, J.A., Ban, N., Moore, P.B. & Steitz, T.A. RNA tertiary interactions in the large ribosomal subunit: The A-minor motif. Proc. Natl. Acad. Sci. USA 98, 4899-4903 (2001).
20. Borer, P.N. et al. Proton NMR and structural features of a 24-nucleotide RNA hairpin. Biochemistry 34, 6488-6503 (1995).
21. Lynch, S.R. & Puglisi, J.D. Structure of a eukaryotic decoding region A-site RNA. J. Mol. Biol. 306, 1023-1035 (2001).
22. Greenbaum, N.L., Radhakrishnan, I., Patel, D. J. & Hirsh, D. Solution structure of the donor site of a trans-splicing RNA. Structure 4, 725-733 (1996).
23. Ennifar, E. et al. The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges. Structure 7, 1439-1449 (1999).
24. Portman, S., Grimm, S., Workman, C., Usman, N. & Egli, M. Crystal structures of an A-form duplex with single-adenosine bulges and a conformational basis for site-specific RNA self-cleavage. Chem. Biol. 3, 173-184 (1996).
25. Hermann, T. & Patel, D. RNA bulges as architectural and recognition motifs. Structure 8, R47-R54 (2000).
26. Berglund, J.A., Rosbash, M. & Schultz, S.C. Crystal structure of a model branchpoint U2 snRNA duplex containing bulged adenosines. RNA 7, 682-691 (2001).
27. phe from hist mutants: A structural role for pseudouridine. Biochemistry 30, 4223-4231 (1991).
28. Yarian, C.S. et al. Structural and functional roles of the N1- and N3-protons of Ψ at tRNA's position 39. Nucleic Acids Res. 27, 3543-3549 (1999).
29. Newby, M.I. & Greenbaum, N.L. Investigation of Overhauser effects between pseudouridine and water protons in RNA helices. Proc. Natl. Acad. Sci. USA 99, 12697-12702 (2002).
30. Hornig, H., Aebi, M. & Weissman, C. Effect of mutations at the lariat branch acceptor site on β-globin pre-messenger RNA splicing in vitro. Nature, 324, 589-591 (1986).
31. Query, C., Strobel, S. & Sharp, P. Three recognition events at the branch site adenosine. EMBO J. 15, 1392-1402 (1996).
32. Michel F., Hanna, M., Green, R., Bartel, D.P. & Szostak, J.W. The guanosine binding site of the Tetrahymena ribozyme. Nature 342, 391-395 (2002).
33. Yarus, M., Illangesekare, M. & Christian, E. Selection of small molecules by the Tetrahymena catalytic center. J. Mol. Biol. 222, 995-1012 (1991).
34. Kitamura, A. et al. Solution structure of an RNA fragment with the P7/P9.0 region and the 3Ψ-terminal guanosine of the Tetrahymena group I intron. RNA 8, 440-451 (2002).
35. Been, M.D., & Perrotta, A.T. Group I intron self-splicing with adenosine: Evidence for a single nucleoside-binding site. Science 252, 434-437 (1991).
36. Zhang, L. & Doudna, J.A. Structural insights into group II intron catalysis and branch site selection. Science 295, 2084-2087 (2002).
37. Massenet, S. & Branlant, C. A limited number of pseudouridine residues in the human atac spliceosomal U snRNAs as compared to human major spliceosomal U snRNAs. RNA 5, 1495-1503 (1999).
38. Wijmenga, S., Mooren, M. & Hilbers, C. in NMR of Macromolecules: A Practical Approach (ed. Roberts, G.C.K.) 207-288 (Oxford University Press, Oxford; 1993).
39. Hwang, T.-L., Mori, S., Shaka, A.J. & van Zijl, P.C.M. Application of phase-modulated CLEAN chemical EXchange spectroscopy (CELANEX-PM) to detect water-protein proton exchange and intermolecular NOEs. J. Am. Chem. Soc. 119, 6203-6204 (1997).
40. Rice, L.M. & Brünger, A.T. Torsion angle dynamics - Reduced variable conformational sampling enhances crystallographic structure refinement. Proteins 19, 277-290 (1994).
41. Stein, E.G., Rice, L.M. & Brünger, A.T. Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation. J. Magn. Reson. 124, 154-164 (1997).
42. Brünger, A.T. X-PLOR Version 3.851: A System for Crystallography and NMR (Yale University Press, New Haven; 1996).
43. Ferrin, T.E., Huang, C.C., Jarvis, L.E. & Langridge, R. The MIDAS display system. J. Mol. Graph. 6, 13-27 (1988).
44. Huang, C.C., Pettersen, E.F., Klein, T.E., Ferrin, T.E. & Langridge, R. Conic: A fast renderer for space-filling molecules with shadows. J. Mol. Graph. 9, 230-236 (1991).
45. Varani, G., Aboul-ela, F. & Allain, F.H.-T. NMR investigation of RNA structure. Prog. Nucl. Magn. Reson. Spec. 29, 51-127 (1996).
46. 31P chemical shift as a probe of structural motifs in RNA. J. Magn. Reson. B 103, 82-86 (1994).
47. Hall, K. & McLaughlin, L. Properties of U1/mRNA 5′ splice site duplex containing pseudouridine as measured by thermodynamic and NMR methods. Biochemistry 30, 1795-1801 (1991).