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Structural insights into amino acid binding and gene control by a lysine riboswitch

Nature volume 455, pages 1263–1267 (2008)Cite this article

Abstract

In bacteria, the intracellular concentration of several amino acids is controlled by riboswitches1,2,3,4. One of the important regulatory circuits involves lysine-specific riboswitches, which direct the biosynthesis and transport of lysine and precursors common for lysine and other amino acids1,2,3. To understand the molecular basis of amino acid recognition by riboswitches, here we present the crystal structure of the 174-nucleotide sensing domain of the Thermotoga maritima lysine riboswitch in the lysine-bound (1.9 ångström (Å)) and free (3.1 Å) states. The riboswitch features an unusual and intricate architecture, involving three-helical and two-helical bundles connected by a compact five-helical junction and stabilized by various long-range tertiary interactions. Lysine interacts with the junctional core of the riboswitch and is specifically recognized through shape-complementarity within the elongated binding pocket and through several direct and K+-mediated hydrogen bonds to its charged ends. Our structural and biochemical studies indicate preformation of the riboswitch scaffold and identify conformational changes associated with the formation of a stable lysine-bound state, which prevents alternative folding of the riboswitch and facilitates formation of downstream regulatory elements. We have also determined several structures of the riboswitch bound to different lysine analogues5, including antibiotics, in an effort to understand the ligand-binding capabilities of the lysine riboswitch and understand the nature of antibiotic resistance. Our results provide insights into a mechanism of lysine-riboswitch-dependent gene control at the molecular level, thereby contributing to continuing efforts at exploration of the pharmaceutical and biotechnological potential of riboswitches.

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Figure 1: Overall structure and long-range tertiary interactions of the lysine-bound T. maritima riboswitch.
Figure 2: Structure and interactions in the junctional region of the lysine riboswitch.
Figure 3: Interactions of lysine analogues with the riboswitch.
Figure 4: Probing lysine riboswitch tertiary structure.

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Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates of the X-ray structures of the lysine riboswitch bound to ligands have been deposited in the RCSB Protein Data Bank under the following accession codes: lysine, 3DIL; AEC, 3DIG; l-4-oxalysine, 3DJ0; homoarginine, 3DIQ; and iminoethyl-l-lysine, 3DIR. Codes for other structures are: free state, 3DIS; [Ir(NH3)6]3+-soaked, 3DIO; Cs+-soaked, 3DIM; Tl+-soaked, 3DJ2; Mn2+-soaked, 3DIY; K+-anomalous, 3DIX; and Mg2+-free form, 3DIZ.

References

  1. Sudarsan, N., Wickiser, J. K., Nakamura, S., Ebert, M. S. & Breaker, R. R. An mRNA structure in bacteria that controls gene expression by binding lysine. Genes Dev. 17, 2688–2697 (2003)

    Article  CAS  Google Scholar 

  2. Grundy, F. J., Lehman, S. C. & Henkin, T. M. The L box regulon: lysine sensing by leader RNAs of bacterial lysine biosynthesis genes. Proc. Natl Acad. Sci. USA 100, 12057–12062 (2003)

    Article  CAS  ADS  Google Scholar 

  3. Rodionov, D. A., Vitreschak, A. G., Mironov, A. A. & Gelfand, M. S. Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch? Nucleic Acids Res. 31, 6748–6757 (2003)

    Article  CAS  Google Scholar 

  4. Mandal, M. et al. A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 306, 275–279 (2004)

    Article  CAS  ADS  Google Scholar 

  5. Blount, K. F., Wang, J. X., Lim, J., Sudarsan, N. & Breaker, R. R. Antibacterial lysine analogs that target lysine riboswitches. Nature Chem. Biol. 3, 44–49 (2007)

    Article  CAS  Google Scholar 

  6. Serganov, A. & Patel, D. J. Ribozymes, riboswitches and beyond: regulation of gene expression without proteins. Nature Rev. Genet. 8, 776–790 (2007)

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  9. Chowdhury, S., Maris, C., Allain, F. H. & Narberhaus, F. Molecular basis for temperature sensing by an RNA thermometer. EMBO J. 25, 2487–2497 (2006)

    Article  CAS  Google Scholar 

  10. Dann, C. E. et al. Structure and mechanism of a metal-sensing regulatory RNA. Cell 130, 878–892 (2007)

    Article  CAS  Google Scholar 

  11. 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  ADS  Google Scholar 

  12. 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 

  13. 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  ADS  Google Scholar 

  14. 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 

  15. 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  ADS  Google Scholar 

  16. Thore, S., Leibundgut, M. & Ban, N. Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand. Science 312, 1208–1211 (2006)

    Article  CAS  ADS  Google Scholar 

  17. Edwards, T. E. & Ferre-D’Amare, A. R. Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition. Structure 14, 1459–1468 (2006)

    Article  CAS  Google Scholar 

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

    Article  CAS  ADS  Google Scholar 

  19. Gilbert, S. D., Rambo, R. P., Van Tyne, D. & Batey, R. T. Structure of the SAM-II riboswitch bound to S-adenosylmethionine. Nature Struct. Mol. Biol. 15, 177–182 (2008)

    Article  CAS  Google Scholar 

  20. Weixlbaumer, A. et al. Crystal structure of the ribosome recycling factor bound to the ribosome. Nature Struct. Mol. Biol. 14, 733–737 (2007)

    Article  CAS  Google Scholar 

  21. Blouin, S. & Lafontaine, D. A. A loop–loop interaction and a K-turn motif located in the lysine aptamer domain are important for the riboswitch gene regulation control. RNA 13, 1256–1267 (2007)

    Article  CAS  Google Scholar 

  22. Correll, C. C., Freeborn, B., Moore, P. B. & Steitz, T. A. Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain. Cell 91, 705–712 (1997)

    Article  CAS  Google Scholar 

  23. Leontis, N. B. & Westhof, E. The 5S rRNA loop E: chemical probing and phylogenetic data versus crystal structure. RNA 4, 1134–1153 (1998)

    Article  CAS  Google Scholar 

  24. 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 

  25. Basu, S. et al. A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor. Nature Struct. Biol. 5, 986–992 (1998)

    Article  CAS  Google Scholar 

  26. Feig, A. L. & Uhlenbeck, O. C. in The RNA World Second Edition (eds Gesteland, R. F., Cech, T. R. & Atkins, J. F.) 287–319 (Cold Spring Harbor Laboratory Press, 1999)

    Google Scholar 

  27. Lu, Y., Shevtchenko, T. N. & Paulus, H. Fine-structure mapping of cis-acting control sites in the lysC operon of Bacillus subtilis . FEMS Microbiol. Lett. 92, 23–27 (1992)

    Article  CAS  Google Scholar 

  28. Patte, J. C., Akrim, M. & Mejean, V. The leader sequence of the Escherichia coli lysC gene is involved in the regulation of LysC synthesis. FEMS Microbiol. Lett. 169, 165–170 (1998)

    Article  CAS  Google Scholar 

  29. Ataide, S. F. et al. Mechanisms of resistance to an amino acid antibiotic that targets translation. ACS Chem. Biol. 2, 819–827 (2007)

    Article  CAS  Google Scholar 

  30. de La Fortelle, E. & Bricogne, G. in Methods in Enzymology 472–494 (Academic Press, 1997)

    Google Scholar 

  31. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53, 240–255 (1997)

    Article  CAS  Google Scholar 

  32. Perrakis, A., Morris, R. & Lamzin, V. S. Automated protein model building combined with iterative structure refinement. Nature Struct. Biol. 6, 458–463 (1999)

    Article  CAS  Google Scholar 

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Acknowledgements

We thank personnel of beamline X29 at the Brookhaven National Laboratory and beamlines 24-ID-C/E at the Advanced Photon Source, Argonne National Laboratory, funded by the US Department of Energy. We thank O. Ouerfelli for the synthesis of iridium hexamine. D.J.P. was supported by funds from the National Institutes of Health.

Author Contributions L.H. crystallized the T. maritima lysine riboswitch; A.S. determined the structures and was assisted by L.H. during refinement; A.S. and L.H. performed biochemical experiments; and A.S. and D.J.P. wrote the manuscript. All authors discussed the results and commented on the manuscript.

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  1. Alexander Serganov and Lili Huang: These authors contributed equally to this work.

Authors and Affiliations

  1. Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA ,

    Alexander Serganov, Lili Huang & Dinshaw J. Patel

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  1. Alexander Serganov
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Correspondence to Alexander Serganov or Dinshaw J. Patel.

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Serganov, A., Huang, L. & Patel, D. Structural insights into amino acid binding and gene control by a lysine riboswitch. Nature 455, 1263–1267 (2008). https://doi.org/10.1038/nature07326

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