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

Nature Structural Biology volume 9, pages 958–965 (2002)Cite this article

Abstract

Pairing of a consensus sequence of the precursor (pre)-mRNA intron with a short region of the U2 small nuclear (sn)RNA during assembly of the eukaryotic spliceosome results in formation of a complementary helix of seven base pairs with a single unpaired adenosine residue. The 2′ OH of this adenosine, called the branch site, brings about nucleophilic attack at the pre-mRNA 5′ splice site in the first step of splicing. Another feature of this pairing is the phylogenetic conservation of a pseudouridine (ψ) residue in U2 snRNA nearly opposite the branch site. We show that the presence of this ψ in the pre-mRNA branch-site helix of Saccharomyces cerevisiae induces a dramatically altered architectural landscape compared with that of its unmodified counterpart. The ψ-induced structure places the nucleophile in an accessible position for the first step of splicing.

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Figure 1: Branch site sequences.
Figure 2: 2-Aminopurine (2AP) fluorescence emission spectra.
Figure 3: Structural models of branch site duplexes.
Figure 4: Structural model of ψ-modified branch site duplex.
Figure 5: Comparison of ψBP and uBP.
Figure 6: Comparison of nucleophile positioning in three splicing systems.

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Acknowledgements

We thank K. Hall for helpful discussions about ψ and 2AP, M. Zawrotny for computer support and the laboratory of D. Patel, in particular A. Gorin, for assistance with the initial structure calculation of ψBP. We also thank Y.-T. Yu for sharing new data with us before publication. We acknowledge the National High Magnetic Field Laboratory (Tallahassee, Florida) for NMR facilities and support. M.I.N. is a recipient of a Molecular Biophysics fellowship funded by National Science Foundation Research Training Grant. This work was supported by a National Institutes of Health Grant to N.L.G.

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  1. Institute of Molecular Biophysics, Florida State University, Tallahassee, 32306-4390, Florida, USA

    Meredith I. Newby & Nancy L. Greenbaum

  2. Department of Chemistry and Biochemistry, Florida State University, Tallahassee, 32306-4390, Florida, USA

    Nancy L. Greenbaum

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Correspondence to Nancy L. Greenbaum.

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Newby, M., Greenbaum, N. Sculpting of the spliceosomal branch site recognition motif by a conserved pseudouridine. Nat Struct Mol Biol 9, 958–965 (2002). https://doi.org/10.1038/nsb873

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