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Structure of the SAM-II riboswitch bound to S-adenosylmethionine

Nature Structural & Molecular Biology volume 15, pages 177–182 (2008)Cite this article

Abstract

In bacteria, numerous genes harbor regulatory elements in the 5′ untranslated regions of their mRNA, termed riboswitches, which control gene expression by binding small-molecule metabolites. These sequences influence the secondary and tertiary structure of the RNA in a ligand-dependent manner, thereby directing its transcription or translation. The crystal structure of an S-adenosylmethionine–responsive riboswitch found predominantly in proteobacteria, SAM-II, has been solved to reveal a second means by which RNA interacts with this important cellular metabolite. Notably, this is the first structure of a complete riboswitch containing all sequences associated with both the ligand binding aptamer domain and the regulatory expression platform. Chemical probing of this RNA in the absence and presence of ligand shows how the structure changes in response to S-adenosylmethionine to sequester the ribosomal binding site and affect translational gene regulation.

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Figure 1: Global structure of SAM-II bound to S-adenosylmethionine (SAM).
Figure 2: Detailed structural view of the A minor twist motif and the ligand binding pocket, key tertiary interactions in the ligand-bound structure.
Figure 3: Comparison of the SAM-II (left) and SAM-I (right) binding pocket interactions with S-adenosylmethionine (SAM).
Figure 4: Chemical probing of the structural difference between unliganded and liganded S-adenosylmethionine II (SAM-II).

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References

  1. Winkler, W.C. & Breaker, R.R. Regulation of bacterial gene expression by riboswitches. Annu. Rev. Microbiol. 59, 487–517 (2005).

    Article  CAS  Google Scholar 

  2. Grundy, F.J. & Henkin, T.M. The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in Gram-positive bacteria. Mol. Microbiol. 30, 737–749 (1998).

    Article  CAS  Google Scholar 

  3. Winkler, W.C., Nahvi, A., Sudarsan, N., Barrick, J.E. & Breaker, R.R. An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nat. Struct. Biol. 10, 701–707 (2003).

    Article  CAS  Google Scholar 

  4. Corbino, K.A. et al. Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in α-proteobacteria. Genome Biol. 6, R70 (2005).

    Article  Google Scholar 

  5. Lim, J., Winkler, W.C., Nakamura, S., Scott, V. & Breaker, R.R. Molecular-recognition characteristics of SAM-binding riboswitches. Angew. Chem. Int. Edn. Engl. 45, 964–968 (2006).

    Article  CAS  Google Scholar 

  6. Fuchs, R.T., Grundy, F.J. & Henkin, T.M. The SMK box is a new SAM-binding RNA for translational regulation of SAM synthetase. Nat. Struct. Mol. Biol. 13, 226–233 (2006).

    Article  CAS  Google Scholar 

  7. Fuchs, R.T., Grundy, F.J. & Henkin, T.M. S-adenosylmethionine directly inhibits binding of 30S ribosomal subunits to the SMK box translational riboswitch RNA. Proc. Natl. Acad. Sci. USA 104, 4876–4880 (2007).

    Article  CAS  Google Scholar 

  8. Barrick, J.E. & Breaker, R.R. The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol. 8, R239 (2007).

    Article  Google Scholar 

  9. Montange, R.K. & Batey, R.T. Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Nature 441, 1172–1175 (2006).

    Article  CAS  Google Scholar 

  10. Griffiths-Jones, S. et al. Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res. 33, D121–D124 (2005).

    Article  CAS  Google Scholar 

  11. Venter, J.C. et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66–74 (2004).

    Article  CAS  Google Scholar 

  12. Keel, A.Y., Rambo, R.P., Batey, R.T. & Kieft, J.S. A general strategy to solve the phase problem in RNA crystallography. Structure 15, 761–772 (2007).

    Article  CAS  Google Scholar 

  13. Hilbers, C.W., Michiels, P.J.A. & Heus, H.A. New developments in structure determination of pseudoknots. Biopolymers 48, 137–158 (1998).

    Article  CAS  Google Scholar 

  14. Nonin-Lecomte, S., Felden, B. & Dardel, F. NMR structure of the Aquifex aeolicustmRNA pseudoknot PK1: new insights into the recoding event of the ribosomal trans-translation. Nucl. Acids Res. 34, 1847–1853 (2006).

    Article  CAS  Google Scholar 

  15. Theimer, C.A., Blois, C.A. & Feigon, J. Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function. Mol. Cell 17, 671–682 (2005).

    Article  CAS  Google Scholar 

  16. Chen, X. et al. Structural and functional studies of retroviral RNA pseudoknots involved in ribosomal frameshifting: nucleotides at the junction of the two stems are important for efficient ribosomal frameshifting. EMBO J. 14, 842–852 (1995).

    Article  CAS  Google Scholar 

  17. Pallan, P.S. et al. Crystal structure of a luteoviral RNA pseudoknot and model for a minimal ribosomal frameshifting motif. Biochemistry 44, 11315–11322 (2005).

    Article  CAS  Google Scholar 

  18. Su, L., Chen, L., Egli, M., Berger, J.M. & Rich, A. Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot. Nat. Struct. Biol. 6, 285–292 (1999).

    Article  CAS  Google Scholar 

  19. Doherty, E.A., Batey, R.T., Masquida, B. & Doudna, J.A. A universal mode of helix packing in RNA. Nat. Struct. Biol. 8, 339–343 (2001).

    Article  CAS  Google Scholar 

  20. Cochrane, J.C., Lipchock, S.V. & Strobel, S.A. Structural investigation of the glmS ribozyme bound to its catalytic cofactor. Chem. Biol. 14, 97–105 (2007).

    Article  CAS  Google Scholar 

  21. Klein, D.J. & Ferre-D'Amare, A.R. Structural basis of glmS ribozyme activation by glucosamine-6-phosphate. Science 313, 1752–1756 (2006).

    Article  CAS  Google Scholar 

  22. Battle, D.J. & Doudna, J.A. Specificity of RNA-RNA helix recognition. Proc. Natl. Acad. Sci. USA 99, 11676–11681 (2002).

    Article  CAS  Google Scholar 

  23. Nissen, P., 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).

    Article  CAS  Google Scholar 

  24. Lim, J., Winkler, W.C., Nakamura, S., Scott, V. & Breaker, R.R. Molecular-recognition characteristics of SAM-binding riboswitches. Angew. Chem. Int. Edn Engl. 45, 964–968 (2006).

    Article  CAS  Google Scholar 

  25. Edwards, T.E., Klein, D.J. & Ferre-D'Amare, A.R. Riboswitches: small-molecule recognition by gene regulatory RNAs. Curr. Opin. Struct. Biol. 17, 273–279 (2007).

    Article  CAS  Google Scholar 

  26. Wilkinson, K.A., Merino, E.J. & Weeks, K.M. Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nat. Protoc. 1, 1610–1616 (2006).

    Article  CAS  Google Scholar 

  27. Moazed, D. & Noller, H.F. Transfer RNA shields specific nucleotides in 16S ribosomal RNA from attack by chemical probes. Cell 47, 985–994 (1986).

    Article  CAS  Google Scholar 

  28. Batey, R.T., Gilbert, S.D. & Montange, R.K. Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature 432, 411–415 (2004).

    Article  CAS  Google Scholar 

  29. Martick, M. & Scott, W.G. Tertiary contacts distant from the active site prime a ribozyme for catalysis. Cell 126, 309–320 (2006).

    Article  CAS  Google Scholar 

  30. Adams, P.L., Stahley, M.R., Kosek, A.B., Wang, J. & Strobel, S.A. Crystal structure of a self-splicing group I intron with both exons. Nature 430, 45–50 (2004).

    Article  CAS  Google Scholar 

  31. Brierley, I., Pennell, S. & Gilbert, R.J. Viral RNA pseudoknots: versatile motifs in gene expression and replication. Nat. Rev. Microbiol. 5, 598–610 (2007).

    Article  CAS  Google Scholar 

  32. Moriarty, T.J., Marie-Egyptienne, D.T. & Autexier, C. Functional organization of repeat addition processivity and DNA synthesis determinants in the human telomerase multimer. Mol. Cell. Biol. 24, 3720–3733 (2004).

    Article  CAS  Google Scholar 

  33. Tzfati, Y., Knight, Z., Roy, J. & Blackburn, E.H. A novel pseudoknot element is essential for the action of a yeast telomerase. Genes Dev. 17, 1779–1788 (2003).

    Article  CAS  Google Scholar 

  34. Winkler, W.C. & Breaker, R.R. Genetic control by metabolite-binding riboswitches. ChemBioChem 4, 1024–1032 (2003).

    Article  CAS  Google Scholar 

  35. Gilbert, S.D. & Batey, R.T. Riboswitches: fold and function. Chem. Biol. 13, 805–807 (2006).

    Article  CAS  Google Scholar 

  36. Nudler, E. & Mironov, A.S. The riboswitch control of bacterial metabolism. Trends Biochem. Sci. 29, 11–17 (2004).

    Article  CAS  Google Scholar 

  37. Serganov, A. et al. Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. Chem. Biol. 11, 1729–1741 (2004).

    Article  CAS  Google Scholar 

  38. Mironov, A.S. et al. Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria. Cell 111, 747–756 (2002).

    Article  CAS  Google Scholar 

  39. Serganov, A., Polonskaia, A., Phan, A.T., Breaker, R.R. & Patel, D.J. Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch. Nature 441, 1167–1171 (2006).

    Article  CAS  Google Scholar 

  40. Zengel, J.M. & Lindahl, L. Diverse mechanisms for regulating ribosomal protein synthesis in Escherichia coli. Prog. Nucleic Acid Res. Mol. Biol. 47, 331–370 (1994).

    Article  CAS  Google Scholar 

  41. Merianos, H.J., Wang, J. & Moore, P.B. The structure of a ribosomal protein S8/spc operon mRNA complex. RNA 10, 954–964 (2004).

    Article  CAS  Google Scholar 

  42. Weinberg, Z. et al. Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Res. 35, 4809–4819 (2007).

    Article  CAS  Google Scholar 

  43. Gilbert, S.D., Stoddard, C.D., Wise, S.J. & Batey, R.T. Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain. J. Mol. Biol. 359, 754–768 (2006).

    Article  CAS  Google Scholar 

  44. DeLano, W.L. The PyMOL Molecular Graphics System. (2002).

  45. Kjems, J., Egebjerg, J. & Christiansen, J. Analysis of RNA–Protein Complexes in vitro (Elsevier, Amsterdam, 1998).

    Google Scholar 

  46. Das, R., Laederach, A., Pearlman, S.M., Herschlag, D. & Altman, R.B. SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. RNA 11, 344–354 (2005).

    Article  CAS  Google Scholar 

  47. Leontis, N.B. & Westhof, E. Geometric nomenclature and classification of RNA base pairs. RNA 7, 499–512 (2001).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank S. Edwards for maintaining the home X-ray source, A. Edwards for critical comments on the manuscript and J. Kieft for useful discussions and input on this project. This work was supported by grants from the US National Institutes of Health (GM 073850) and the American Heart Association (Scientist Development Grant) to R.T.B.

Author information

Authors and Affiliations

  1. Department of Chemistry and Biochemistry, Campus Box 215, University of Colorado, Boulder, 80309, Colorado, USA

    Sunny D Gilbert, Daria Van Tyne & Robert T Batey

  2. Life Science Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Building 6 Room 2105, Berkeley, 94720, California, USA

    Robert P Rambo

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  2. Robert P Rambo
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  4. Robert T Batey
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Contributions

S.D.G. and R.T.B. conceived and carried out the experiments, solved the structure and wrote the paper. R.P.R. provided critical crystallographic expertise throughout the data collection and refinement process. D.V.T. assisted in screening the initial RNA library to find a crystallizable RNA variant.

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Correspondence to Robert P Rambo.

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Supplementary Figures 1–7, Supplementary Table 1 and Methods (PDF 752 kb)

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Gilbert, S., Rambo, R., Van Tyne, D. et al. Structure of the SAM-II riboswitch bound to S-adenosylmethionine. Nat Struct Mol Biol 15, 177–182 (2008). https://doi.org/10.1038/nsmb.1371

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