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Structure and function of archaeal box C/D sRNP core proteins

Nature Structural & Molecular Biology volume 10, pages 256–263 (2003)Cite this article

Abstract

Nop56p and Nop58p are two core proteins of the box C/D snoRNPs that interact concurrently with fibrillarin and snoRNAs to function in enzyme assembly and catalysis. Here we report the 2.9 Å resolution co-crystal structure of an archaeal homolog of Nop56p/Nop58p, Nop5p, in complex with fibrillarin from Archaeoglobus fulgidus (AF) and the methyl donor S-adenosyl-L-methionine. The N-terminal domain of Nop5p forms a complementary surface to fibrillarin that serves to anchor the catalytic subunit and to stabilize cofactor binding. A coiled coil in Nop5p mediates dimerization of two fibrillarin–Nop5p heterodimers for optimal interactions with bipartite box C/D RNAs. Structural analysis and complementary biochemical data demonstrate that the conserved C-terminal domain of Nop5p harbors RNA-binding sites. A model of box C/D snoRNP assembly is proposed based on the presented structural and biochemical data.

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Figure 1: Crystal structure of the AF fibrillarin–Nop5p complex.
Figure 2: Sequence alignment of AF Nop5p against its homologs retrieved from SWISS-PROT database (http://us.expasy.org/sprot/).
Figure 3: The fibrillarin–Nop5p interface.
Figure 4: Dissecting the functions of Nop5p domains.
Figure 5: The C-terminal domain of Nop5p is important for binding to box C/D RNA.
Figure 6: AdoMet binding to fibrillarin.
Figure 7: A proposed model of archaeal box C/D snoRNP assembly.

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References

  1. Maxwell, E.S. & Fournier, M.J. The small nucleolar RNAs. Annu. Rev. Biochem. 64, 897–934 (1995).

    Article  CAS  Google Scholar 

  2. Lafontaine, D.L. & Tollervey, D. Synthesis and assembly of the box C+D small nucleolar RNPs. Mol. Cell. Biol. 20, 2650–2659 (2000).

    Article  CAS  Google Scholar 

  3. Weinstein, L.B. & Steitz, J.A. Guided tours: from precursor snoRNA to functional snoRNP. Curr. Opin. Cell Biol. 11, 378–384 (1999).

    Article  CAS  Google Scholar 

  4. Kiss, T. Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs. EMBO J. 20, 3617–3622 (2001).

    Article  CAS  Google Scholar 

  5. Terns, M.P. & Terns, R.M. Small nucleolar RNAs: versatile trans-acting molecules of ancient evolutionary origin. Gene Expr. 10, 17–39 (2002).

    CAS  PubMed  Google Scholar 

  6. Omer, A.D. et al. Homologs of small nucleolar RNAs in Archaea. Science 288, 517–522 (2000).

    Article  CAS  Google Scholar 

  7. d'Orval, B.C., Bortolin, M.L., Gaspin, C. & Bachellerie, J.P. Box C/D RNA guides for the ribose methylation of archaeal tRNAs. The tRNATrp intron guides the formation of two ribose-methylated nucleosides in the mature tRNATrp. Nucleic Acids Res. 29, 4518–4529 (2001).

    Article  CAS  Google Scholar 

  8. Dragon, F. et al. A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesis. Nature 417, 967–970 (2002).

    Article  CAS  Google Scholar 

  9. Kiss-Laszlo, Z., Henry, Y., Bachellerie, J.P., Caizergues-Ferrer, M. & Kiss, T. Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. Cell 85, 1077–1088 (1996).

    Article  CAS  Google Scholar 

  10. Gautier, T., Berges, T., Tollervey, D. & Hurt, E. Nucleolar KKE/D repeat proteins Nop56p and Nop58p interact with Nop1p and are required for ribosome biogenesis. Mol. Cell. Biol. 17, 7088–7098 (1997).

    Article  CAS  Google Scholar 

  11. Weidenhammer, E.M., Ruiz-Noriega, M. & Woolford J.L. Jr. Prp31p promotes the association of the U4/U6 × U5 tri-snRNP with prespliceosomes to form spliceosomes in Saccharomyces cerevisiae. Mol. Cell. Biol. 17, 3580–3588 (1997).

    Article  CAS  Google Scholar 

  12. Weidenhammer, E.M., Singh, M., Ruiz-Noriega, M. & Woolford J.L. Jr. The PRP31 gene encodes a novel protein required for pre-mRNA splicing in Saccharomyces cerevisiae. Nucleic Acids Res. 24, 1164–1170 (1996).

    Article  CAS  Google Scholar 

  13. von Kries, J.P., Buhrmester, H. & Stratling, W.H. A matrix/scaffold attachment region binding protein: identification, purification, and mode of binding. Cell 64, 123–135 (1991).

    Article  CAS  Google Scholar 

  14. van Drunen, C.M. et al. A bipartite sequence element associated with matrix/scaffold attachment regions. Nucleic Acids Res. 27, 2924–2930 (1999).

    Article  CAS  Google Scholar 

  15. Omer, A.D., Ziesche, S., Ebhardt, H. & Dennis, P.P. In vitro reconstitution and activity of a C/D box methylation guide ribonucleoprotein complex. Proc. Natl. Acad. Sci. USA 99, 5289–5294 (2002).

    Article  CAS  Google Scholar 

  16. Niewmierzycka, A. & Clarke, S. S-adenosylmethionine-dependent methylation in Saccharomyces cerevisiae. Identification of a novel protein arginine methyltransferase. J. Biol. Chem. 274, 814–824 (1999).

    Article  CAS  Google Scholar 

  17. Wang, H., Boisvert, D., Kim, K.K., Kim, R. & Kim, S.H. Crystal structure of a fibrillarin homologue from Methanococcus jannaschii, a hyperthermophile, at 1.6 Å resolution. EMBO J. 19, 317–323 (2000).

    Article  CAS  Google Scholar 

  18. Newman, D.R., Kuhn, J.F., Shanab, G.M. & Maxwell, E.S. Box C/D snoRNA-associated proteins: two pairs of evolutionarily ancient proteins and possible links to replication and transcription. Rna 6, 861–879 (2000).

    Article  CAS  Google Scholar 

  19. Nottrott, S. et al. Functional interaction of a novel 15.5kD [U4/U6●U5] tri-snRNP protein with the 5′ stem-loop of U4 snRNA. EMBO J. 18, 6119–6133 (1999).

    Article  CAS  Google Scholar 

  20. Watkins, N.J. et al. A common core RNP structure shared between the small nucleoar box C/D RNPs and the spliceosomal U4 snRNP. Cell 103, 457–466 (2000).

    Article  CAS  Google Scholar 

  21. Klein, D.J., Schmeing, T.M., Moore, P.B. & Steitz, T.A. The kink-turn: a new RNA secondary structure motif. EMBO J. 20, 4214–4221 (2001).

    Article  CAS  Google Scholar 

  22. Kuhn, J.F., Tran, E.J. & Maxwell, E.S. Archaeal ribosomal protein L7 is a functional homolog of the eukaryotic 15.5kD/Snu13p snoRNP core protein. Nucleic Acids Res. 30, 931–941 (2002).

    Article  CAS  Google Scholar 

  23. Cahill, N.M. et al. Site-specific cross-linking analyses reveal an asymmetric protein distribution for a box C/D snoRNP. EMBO J. 21, 3816–3828 (2002).

    Article  CAS  Google Scholar 

  24. Cheng, X. & Roberts, R.J. AdoMet-dependent methylation, DNA methyltransferases and base flipping. Nucleic Acids Res. 29, 3784–3795 (2001).

    Article  CAS  Google Scholar 

  25. Tollervey, D., Lehtonen, H., Jansen, R., Kern, H. & Hurt, E.C. Temperature-sensitive mutations demonstrate roles for yeast fibrillarin in pre-rRNA processing, pre-rRNA methylation, and ribosome assembly. Cell 72, 443–457 (1993).

    Article  CAS  Google Scholar 

  26. Burkhard, P., Stetefeld, J. & Strelkov, S.V. Coiled coils: a highly versatile protein folding motif. Trends Cell Biol. 11, 82–88 (2001).

    Article  CAS  Google Scholar 

  27. Kohn, W.D., Mant, C.T. & Hodges, R.S. α-helical protein assembly motifs. J. Biol. Chem. 272, 2583–2586 (1997).

    Article  CAS  Google Scholar 

  28. Soelaiman, S., Jakes, K., Wu, N., Li, C. & Shoham, M. Crystal structure of colicin E3: implications for cell entry and ribosome inactivation. Mol. Cell 8, 1053–1062 (2001).

    Article  CAS  Google Scholar 

  29. Soisson, S.M., MacDougall-Shackleton, B., Schleif, R. & Wolberger, C. The 1.6 Å crystal structure of the AraC sugar-binding and dimerization domain complexed with d-fucose. J. Mol. Biol. 273, 226–237 (1997).

    Article  CAS  Google Scholar 

  30. Lowe, T.M. & Eddy, S.R. A computational screen for methylation guide snoRNAs in yeast. Science 283, 1168–1171 (1999).

    Article  CAS  Google Scholar 

  31. Gaspin, C., Cavaille, J., Erauso, G. & Bachellerie, J.P. Archaeal homologs of eukaryotic methylation guide small nucleolar RNAs: lessons from the Pyrococcus genomes. J. Mol. Biol. 297, 895–906 (2000).

    Article  CAS  Google Scholar 

  32. Li, H., Trotta, C.R. & Abelson, J. Crystal structure and evolution of a transfer RNA splicing enzyme. Science 280, 279–284 (1998).

    Article  CAS  Google Scholar 

  33. Brunger, A.T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998).

    Article  CAS  Google Scholar 

  34. Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjeldgaard, M. Improved methods for binding protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991).

    Article  Google Scholar 

  35. Milligan, J.F., Groebe, D.R., Witherell, G.W. & Uhlenbeck, O.C. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 15, 8783–8798 (1987).

    Article  CAS  Google Scholar 

  36. Wyman, J. & Gill, S.J. Binding and linkage: functional chemistry of biological macromolecules, xiii (University Science Books, Mill Valley; 1990).

    Google Scholar 

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Acknowledgements

We thank T. Somasundaram and J. Hildenbrand for assistance with data collection, C. Ogata for beamtime allocation at the Brookhaven National Laboratory and National Synchrotron Light Source, and E.K.H. Allen and M. Jackson for reading the manuscript. This work was supported in part by a grant from the Florida Department of Health to H.L.

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  1. Department of Chemistry and Biochemistry, Institute of Molecular Biophysics, Florida State University, Tallahassee, 32306, Florida, USA

    Mohamed Aittaleb, Rumana Rashid, Qiong Chen & Hong Li

  2. Department of Microbiology, The Ohio State University, Columbus, 43210, Ohio, USA

    John R. Palmer & Charles J. Daniels

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Correspondence to Hong Li.

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Aittaleb, M., Rashid, R., Chen, Q. et al. Structure and function of archaeal box C/D sRNP core proteins. Nat Struct Mol Biol 10, 256–263 (2003). https://doi.org/10.1038/nsb905

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