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Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch

Nature volume 441, pages 1167–1171 (2006)Cite this article

Abstract

Riboswitches are metabolite-sensing RNAs, typically located in the non-coding portions of messenger RNAs, that control the synthesis of metabolite-related proteins1,2,3. Here we describe a 2.05 Å crystal structure of a riboswitch domain from the Escherichia coli thiM mRNA4 that responds to the coenzyme thiamine pyrophosphate (TPP). TPP is an active form of vitamin B1, an essential participant in many protein-catalysed reactions5. Organisms from all three domains of life6,7,8,9, including bacteria, plants and fungi, use TPP-sensing riboswitches to control genes responsible for importing or synthesizing thiamine and its phosphorylated derivatives, making this riboswitch class the most widely distributed member of the metabolite-sensing RNA regulatory system. The structure reveals a complex folded RNA in which one subdomain forms an intercalation pocket for the 4-amino-5-hydroxymethyl-2-methylpyrimidine moiety of TPP, whereas another subdomain forms a wider pocket that uses bivalent metal ions and water molecules to make bridging contacts to the pyrophosphate moiety of the ligand. The two pockets are positioned to function as a molecular measuring device that recognizes TPP in an extended conformation. The central thiazole moiety is not recognized by the RNA, which explains why the antimicrobial compound pyrithiamine pyrophosphate targets this riboswitch and downregulates the expression of thiamine metabolic genes. Both the natural ligand and its drug-like analogue stabilize secondary and tertiary structure elements that are harnessed by the riboswitch to modulate the synthesis of the proteins coded by the mRNA. In addition, this structure provides insight into how folded RNAs can form precision binding pockets that rival those formed by protein genetic factors.

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Figure 1: Structural models of a TPP riboswitch and its ligands.
Figure 2: Structure and interactions in the TPP-binding pocket.
Figure 3: Tertiary interactions defining TPP riboswitch structure and accessibility to the binding pocket.
Figure 4: Structural probing of the TPP riboswitch and implications for TPP-mediated gene repression.

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References

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  3. Soukup, G. A. & Soukup, J. K. Riboswitches exert genetic control through metabolite-induced conformational change. Curr. Opin. Struct. Biol. 14, 344–349 (2004)

    Article  CAS  PubMed  Google Scholar 

  4. Winkler, W., Nahvi, A. & Breaker, R. R. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419, 952–956 (2002)

    Article  ADS  CAS  PubMed  Google Scholar 

  5. Schowen, R. L. in Comprehensive Biological Catalysis Vol. 2 (ed. Sinnott, M.) 217–266 (Academic, San Diego, 1998)

    Google Scholar 

  6. Sudarsan, N., Barrick, J. E. & Breaker, R. R. Metabolite-binding RNA domains are present in the genes of eukaryotes. RNA 9, 644–647 (2003)

    Article  CAS  PubMed  Google Scholar 

  7. Kubodera, T. et al. Thiamine-regulated gene expression of Aspergillius oryzae thiA requires splicing of the intron containing a riboswitch-like domain in the 5′-UTR. FEBS Lett. 555, 516–520 (2003)

    Article  CAS  PubMed  Google Scholar 

  8. Miranda-Rios, J., Navarro, M. & Soberón, M. A. A conserved RNA structure (thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria. Proc. Natl Acad. Sci. USA 98, 9736–9741 (2001)

    Article  ADS  CAS  PubMed  Google Scholar 

  9. Rodionov, D. A., Vitreschak, A. G., Mironov, A. A. & Gelfand, M. S. Comparative genomics of thiamin biosynthesis in prokaryotes. New genes and regulatory mechanisms. J. Biol. Chem. 277, 48949–48959 (2002)

    Article  CAS  PubMed  Google Scholar 

  10. Nahvi, A. et al. Genetic control by a metabolite binding mRNA. Chem. Biol. 9, 1043–1049 (2002)

    Article  CAS  PubMed  Google Scholar 

  11. 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  PubMed  Google Scholar 

  12. Winkler, W. C., Cohen-Chalamish, S. & Breaker, R. R. An mRNA structure that controls gene expression by binding FMN. Proc. Natl Acad. Sci. USA 99, 15908–15913 (2002)

    Article  ADS  CAS  PubMed  Google Scholar 

  13. 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 

  14. Winkler, W. C. Metabolic monitoring by bacterial mRNAs. Arch. Microbiol. 183, 151–159 (2005)

    Article  CAS  PubMed  Google Scholar 

  15. Winkler, W. C., Nahvi, A., Roth, A., Collins, J. A. & Breaker, R. R. Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428, 281–286 (2004)

    Article  ADS  CAS  PubMed  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  17. 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  PubMed  Google Scholar 

  18. Auffinger, P., Bielecki, L. & Westhof, E. Anion binding to nucleic acids. Structure 12, 379–388 (2004)

    Article  CAS  Google Scholar 

  19. Sudarsan, N., Cohen-Chalamish, S., Nakamura, S., Emilsson, G. M. & Breaker, R. R. Thiamine pyrophosphate riboswitches are targets for the antimicrobial compound pyrithiamine. Chem. Biol. 12, 1325–1335 (2005)

    Article  CAS  PubMed  Google Scholar 

  20. Nagaswamy, U. & Fox, G. E. Frequent occurrence of the T-loop RNA folding motif in ribosomal RNAs. RNA 8, 1112–1119 (2002)

    Article  CAS  PubMed  Google Scholar 

  21. Yamauchi, T. et al. Roles of Mg2+ in TPP-dependent riboswitch. FEBS Lett. 579, 2583–2588 (2005)

    Article  CAS  PubMed  Google Scholar 

  22. Brodersen, D. E. et al. The structural basis for the action of the antibiotics tetracycline, pactamycin, and hygromycin B on the 30S ribosomal subunit. Cell 103, 1143–1154 (2000)

    Article  CAS  PubMed  Google Scholar 

  23. Schlunzen, F. et al. Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria. Nature 413, 814–821 (2001)

    Article  ADS  CAS  PubMed  Google Scholar 

  24. Pioletti, M. et al. Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3. EMBO J. 20, 1829–1839 (2001)

    Article  CAS  PubMed  Google Scholar 

  25. 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  Google Scholar 

  26. 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  PubMed  Google Scholar 

  27. Hesselberth, J. R. & Ellington, A. D. A (ribo) switch in the paradigms of genetic regulation. Nature Struct. Biol. 9, 891–893 (2002)

    Article  CAS  PubMed  Google Scholar 

  28. Terwilliger, T. C. & Berendzen, J. Automated MAD and MIR structure solution. Acta Crystallogr. D 55, 849–861 (1999)

    Article  CAS  PubMed  Google Scholar 

  29. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53, 240–245 (1997)

    Article  CAS  PubMed  Google Scholar 

  30. Serganov, A., Polonskaia, A., Ehresmann, B., Ehresmann, C. & Patel, D. J. Ribosomal protein S15 represses its own translation via adaptation of an rRNA-like fold within its mRNA. EMBO J. 22, 1898–1908 (2003)

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank L. Malinina and Y.-R. Yuan for extensive discussions; A. Kazantsev and M. Yusupov for the gift of Os(NH3)6; and M. Becker for assistance with synchrotron data collection on beamline X25 at the Brookhaven National Laboratory, supported by the US Department of Energy. D.J.P. and R.R.B. were supported by funds from the NIH. Author Contributions A.S. was responsible for all structural and biochemical aspects of this project. A.P. participated in RNA preparation and crystallization trials, and A.T.P. participated in NMR experiments. D.J.P., A.S. and R.R.B. co-wrote the paper. All authors discussed the results and commented on the manuscript.

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Authors and Affiliations

  1. Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, 10021, USA

    Alexander Serganov, Anna Polonskaia, Anh Tuân Phan & Dinshaw J. Patel

  2. Department of Molecular, Cellular and Developmental Biology and Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, 06520, USA

    Ronald R. Breaker

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Correspondence to Alexander Serganov or Dinshaw J. Patel.

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Coordinates of the X-ray structure of the TPP-bound riboswitch have been deposited in the RCSB Protein Data Bank under accession code 2GDI. Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.

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This file contains the Supplementary Methods, Supplementary Figures 1–11 and Supplementary Table. (PDF 2910 kb)

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Serganov, A., Polonskaia, A., Phan, A. et al. Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch. Nature 441, 1167–1171 (2006). https://doi.org/10.1038/nature04740

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