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Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine

Nature volume 432, pages 411–415 (2004)Cite this article

Abstract

Riboswitches are genetic regulatory elements found in the 5′ untranslated region of messenger RNA that act in the absence of protein cofactors1,2. They are broadly distributed across bacteria and account for the regulation of more than 2% of all genes in Bacillus subtilis, underscoring their importance in the control of cellular metabolism3. The 5′ untranslated region of many mRNAs of genes involved in purine metabolism and transport contain a guanine-responsive riboswitch that directly binds guanine, hypoxanthine or xanthine to terminate transcription3,4. Here we report the crystal structure at 1.95 Å resolution of the purine-binding domain of the guanine riboswitch from the xpt–pbuX operon of B. subtilis bound to hypoxanthine, a prevalent metabolite in the bacterial purine salvage pathway. This structure reveals a complex RNA fold involving several phylogenetically conserved nucleotides that create a binding pocket that almost completely envelops the ligand. Hypoxanthine functions to stabilize this structure and to promote the formation of a downstream transcriptional terminator element, thereby providing a mechanism for directly repressing gene expression in response to an increase in intracellular concentrations of metabolite.

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Figure 1: Secondary and tertiary structures of the guanine riboswitch–hypoxanthine complex.
Figure 2: Recognition of hypoxanthine (HX) by the guanine-binding domain.
Figure 3: Stabilization of the tertiary architecture.
Figure 4: Estimation of the affinity of the riboswitch for hypoxanthine.

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References

  1. Vitreschak, A. G., Rodionov, D. A., Mironov, A. A. & Gelfand, M. S. Riboswitches: the oldest mechanism for the regulation of gene expression? Trends Genet. 20, 44–50 (2004)

    Article  CAS  PubMed  Google Scholar 

  2. Mandal, M. & Breaker, R. R. Gene regulation by riboswitches. Nature Rev. Mol. Cell. Biol. 5, 451–463 (2004)

    Article  CAS  Google Scholar 

  3. Mandal, M., Boese, B., Barrick, J. E., Winkler, W. C. & Breaker, R. R. Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell 113, 577–586 (2003)

    Article  CAS  PubMed  Google Scholar 

  4. Johansen, L. E., Nygaard, P., Lassen, C., Agerso, Y. & Saxild, H. H. Definition of a second Bacillus subtilis pur regulon comprising the pur and xpt–pbuX operons plus pbuG, nupG (yxjA), and pbuE (ydhL). J. Bacteriol. 185, 5200–5209 (2003)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Ellington, A. D. & Szostak, J. W. In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818–822 (1990)

    Article  ADS  CAS  PubMed  Google Scholar 

  6. Gold, L., Polisky, B., Uhlenbeck, O. & Yarus, M. Diversity of oligonucleotide functions. Annu. Rev. Biochem. 64, 763–797 (1995)

    Article  CAS  PubMed  Google Scholar 

  7. Silverman, S. K. Rube Goldberg goes (ribo)nuclear? Molecular switches and sensors made from RNA. RNA 9, 377–383 (2003)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Seetharaman, S., Zivarts, M., Sudarsan, N. & Breaker, R. R. Immobilized RNA switches for the analysis of complex chemical and biological mixtures. Nature Biotechnol. 19, 336–341 (2001)

    Article  CAS  Google Scholar 

  9. Zimmermann, G. R., Jenison, R. D., Wick, C. L., Simmorre, J.-P. & Pardi, A. Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA. Nature Struct. Biol. 4, 644–649 (1997)

    Article  CAS  PubMed  Google Scholar 

  10. Fan, P., Suri, A. K., Fiala, R., Live, D. & Patel, D. J. Molecular recognition in the FMN–RNA aptamer complex. J. Mol. Biol. 258, 480–500 (1996)

    Article  CAS  PubMed  Google Scholar 

  11. Baugh, C., Grate, D. & Wilson, C. 2.8 Å crystal structure of the malachite green aptamer. J. Mol. Biol. 301, 117–128 (2000)

    Article  CAS  PubMed  Google Scholar 

  12. Koizumi, M., Soukup, G. A., Kerr, J. N. & Breaker, R. R. Allosteric selection of ribozymes that respond to the second messengers cGMP and cAMP. Nature Struct. Biol. 6, 1062–1071 (1999)

    Article  CAS  PubMed  Google Scholar 

  13. Leulliot, N. & Varani, G. Current topics in RNA–protein recognition: control of specificity and biological function through induced fit and conformational capture. Biochemistry 40, 7947–7956 (2001)

    Article  CAS  PubMed  Google Scholar 

  14. Williamson, J. R. Induced fit in RNA–protein recognition. Nature Struct. Biol. 7, 834–837 (2000)

    Article  CAS  PubMed  Google Scholar 

  15. Mandal, M. & Breaker, R. R. Adenine riboswitches and gene activation by disruption of a transcription terminator. Nature Struct. Mol. Biol. 11, 29–35 (2004)

    Article  CAS  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  17. 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  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  18. Cate, J. H. et al. RNA tertiary structure mediation by adenosine platforms. Science 273, 1696–1699 (1996)

    Article  ADS  CAS  PubMed  Google Scholar 

  19. Correll, C. C., Beneken, J., Plantinga, M. J., Lubbers, M. & Chan, Y. L. The common and the distinctive features of the bulged-G motif based on a 1.04 Å resolution RNA structure. Nucleic Acids Res. 31, 6806–6818 (2003)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Molinaro, M. & Tinoco, I. Jr Use of ultra stable UNCG tetraloop hairpins to fold RNA structures: thermodynamic and spectroscopic applications. Nucleic Acids Res. 23, 3056–3063 (1995)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. De la Pena, M., Gago, S. & Flores, R. Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity. EMBO J. 22, 5561–5570 (2003)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Khvorova, A., Lescoute, A., Westhof, E. & Jayasena, S. D. Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nature Struct. Biol. 10, 708–712 (2003)

    Article  CAS  PubMed  Google Scholar 

  23. Choi, K. Y. & Zalkin, H. Structural characterization and corepressor binding of the Escherichia coli purine repressor. J. Bacteriol. 174, 6207–6214 (1992)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Kieft, J. S. & Batey, R. T. A general method for rapid and nondenaturing purification of RNAs. RNA 10, 988–995 (2004)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Pflugrath, J. W. The finer things in X-ray diffraction data collection. Acta Crystallogr. D 55, 1718–1725 (1999)

    Article  CAS  PubMed  Google Scholar 

  26. Terwilliger, T. SOLVE and RESOLVE: automated structure solution, density modification and model building. J. Synchrotron Radiat. 11, 49–52 (2004)

    Article  CAS  PubMed  Google Scholar 

  27. 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  PubMed  Google Scholar 

  28. Schumacher, M. A., Choi, K. Y., Zalkin, H. & Brennan, R. G. Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by α helices. Science 266, 763–770 (1994)

    Article  ADS  CAS  PubMed  Google Scholar 

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Acknowledgements

We thank S. Edwards for maintaining and managing the Biochemistry Division X-ray Crystallography facility; and T. Cech, A. Pardi, D. Wuttke, J. Kieft and R. Rambo for discussions and comments on the manuscript. This work was funded in part from a grant from the Research Corporation and the University of Colorado Butcher Biotechnology Initiative. S.D.G. was supported in part by a NIH predoctoral training grant.

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

    Robert T. Batey, Sunny D. Gilbert & Rebecca K. Montange

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  1. Robert T. Batey
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Correspondence to Robert T. Batey.

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Batey, R., Gilbert, S. & Montange, R. Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature 432, 411–415 (2004). https://doi.org/10.1038/nature03037

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