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Riboswitches as antibacterial drug targets

Nature Biotechnology volume 24, pages 1558–1564 (2006)Cite this article

Abstract

New validated cellular targets are needed to reinvigorate antibacterial drug discovery. This need could potentially be filled by riboswitches—messenger RNA (mRNA) structures that regulate gene expression in bacteria. Riboswitches are unique among RNAs that serve as drug targets in that they have evolved to form structured and highly selective receptors for small drug-like metabolites. In most cases, metabolite binding to the receptor represses the expression of the gene(s) encoded by the mRNA. If a new metabolite analog were designed that binds to the receptor, the gene(s) regulated by that riboswitch could be repressed, with a potentially lethal effect to the bacteria. Recent work suggests that certain antibacterial compounds discovered decades ago function at least in part by targeting riboswitches. Herein we will summarize the experiments validating riboswitches as drug targets, describe the existing technology for riboswitch drug discovery and discuss the challenges that may face riboswitch drug discoverers.

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Figure 1: TPP-binding riboswitches regulate gene expression.
Figure 2: The distribution of known riboswitch classes in selected bacterial pathogens.
Figure 3: Structural models of ligand-bound riboswitch receptors.
Figure 4: The chemical structures of riboswitch-binding natural metabolites (left) and antibacterial metabolite analogs (right).

References

  1. Theuretzbacher, U. & Toney, J.H. Nature's clarion call of antibacterial resistance: are we listening? Curr. Opin. Investig. Drugs 7, 158–166 (2006).

    CAS  PubMed  Google Scholar 

  2. D'Costa, V.M., McGrann, K.M., Hughes, D.W. & Wright, G.D. Sampling the antibiotic resistome. Science 311, 374–377 (2006).

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  4. Tucker, B.J. & Breaker, R.R. Riboswitches as versatile gene control elements. Curr. Opin. Struct. Biol. 15, 342–348 (2005).

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  9. 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).

    CAS  PubMed  Google Scholar 

  10. Zhang, R., Ou, H.-Y. & Zhang, C.-T. DEG, a database of essential genes. Nucleic Acids Res. 32, D271–D272 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Forsyth, R.A. et al. A genome-wide strategy for the identification of essential genes in Staphylococcus aureus. Mol. Microbiol. 43, 1387–1400 (2002).

    CAS  PubMed  Google Scholar 

  12. Dunman, P.M. et al. Transcription profiling-based identification of Staphylococcus aureus genes regulated by the agr and/or sarA loci. J. Bacteriol. 183, 7341–7353 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Epshtein, V., Mironov, A.S. & Nudler, E. The riboswitch-mediated control of sulfur metabolism in bacteria. Proc. Natl. Acad. Sci. USA 100, 5052–5056 (2003).

    CAS  PubMed  Google Scholar 

  14. Murphy, B.A., Grundy, F.J. & Henkin, T.M. Prediction of gene function in methylthioadenosine recycling from regulatory signals. J. Bacteriol. 184, 2314–2318 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. 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).

    CAS  PubMed  Google Scholar 

  16. Nahvi, A., Barrick, J.E. & Breaker, R.R. Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes. Nucleic Acids Res. 32, 143–150 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Monaghan, R.L. & Barrett, J.F. Antibacterial drug discovery-then, now and the genomics future. Biochem. Pharmacol. 71, 901–909 (2006).

    CAS  PubMed  Google Scholar 

  18. Knowles, D.J., Foloppe, N., Matassova, N.B. & Murchie, A.I. The bacterial ribosome, a promising focus for structure-based drug design. Curr. Opin. Pharmacol. 2, 501–506 (2002).

    CAS  PubMed  Google Scholar 

  19. Steitz, T.A. On the structural basis of peptide-bond formation and antibiotic resistance from atomic structures of the large ribosomal subunit. FEBS Lett. 579, 955–958 (2005).

    CAS  PubMed  Google Scholar 

  20. Zaman, G.J.R. & Michiels, P.J.A. Targeting RNA with small molecule drugs in Trends in RNA Research (ed. McNamara, P.) 1–21 (Nova Science Publishers, Inc., Hauppauge, NY, 2006).

    Google Scholar 

  21. Hermann, T. & Tor, Y. RNA as a target for small-molecule therapeutics. Expert. Opin. Ther. Pat. 15, 49–62 (2005).

    CAS  Google Scholar 

  22. 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).

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  24. 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).

    CAS  PubMed  Google Scholar 

  25. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  28. 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).

    CAS  Google Scholar 

  29. Robbins, W.J. The pyridine analog of thiamine and the growth of fungi. Proc. Natl. Acad. Sci. USA 27, 419–422 (1941).

    CAS  PubMed  Google Scholar 

  30. Woolley, D.W. & White, A.G.C. Selective reversible inhibition of microbial growth with pyrithiamine. J. Exp. Med. 78, 489–497 (1943).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Iwashima, A., Wakabayashi, Y. & Nose, Y. Formation of thiamine pyrophosphate in brain tissue. J. Biochem. 79, 845–847 (1976).

    CAS  PubMed  Google Scholar 

  32. Shiota, T., Folk, J.E. & Tietze, F. Inhibition of lysine utilization in bacteria by S-(beta-aminoethyl) cysteine and its reversal by lysine peptides. Arch. Biochem. Biophys. 77, 372–377 (1958).

    CAS  PubMed  Google Scholar 

  33. McCord, T., Ravel, J., Skinner, C. & Shive, W. DL-4-oxalysine, an inhibitory analog of lysine. J. Am. Chem. Soc. 79, 5693–5696 (1957).

    CAS  Google Scholar 

  34. Blount, K.F., Wang, X.J., Lim, J., Sudarsan, N. & Breaker, R.R. Antibacterial compounds that target lysine riboswitches. Nat. Chem. Biol. in the press (2007).

  35. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Vold, B., Szulmajster, J. & Carbone, A. Regulation of dihydropicolinate synthase and aspartate kinase in Bacillus subtilis. J. Bacteriol. 121, 970–974 (1975).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Lu, Y., Shevtchenko, T. & Paulus, H. Fine structure mapping of cis-acting control sites in the lysC operon of Bacillus subtilis. FEMS Microbiol. Lett. 71, 23–27 (1992).

    CAS  PubMed  Google Scholar 

  38. Matsui, K. et al. Riboflavin production by roseoflavin-resistant strains of some bacteria. Agric. Biol. Chem. 46, 2003–2008 (1982).

    CAS  Google Scholar 

  39. Berezovskii, V.M., Stepanov, A.I., Polyakova, N.A., Tulchinskaya, L.S. & Kukanova, A.Y. Studies of a group of allo- and isoallxazine. XLVI. Synthesis and biological specificity of amino analogs. Bioorg. Khim, 3, 521–524 (1977).

    CAS  Google Scholar 

  40. Gelfand, M.S., Mironov, A.A., Jomantas, J., Kozlov, Y.I. & Perumov, D.A. A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes. Trends Genet. 15, 439–442 (1999).

    CAS  PubMed  Google Scholar 

  41. 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).

    CAS  PubMed  Google Scholar 

  42. Burgess, C., O' Connel-Motherway, M., Sybesma, W., Hugenholtz, J. & van Sinderen, D. Riboflavin production in Lactococcus lactis: potential for in situ production of vitamin-enriched foods. Appl. Environ. Microbiol. 70, 5769–5777 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  43. Kreneva, R.A. & Perumov, D.A. Genetic mapping of regulatory mutations of Bacillus subtilis riboflavin operon. Mol. Gen. Genet. 222, 467–469 (1990).

    CAS  PubMed  Google Scholar 

  44. Kil, Y.V., Mironov, V.N., Gorishin, I., Kreneva, R.A. & Perumov, D.A. Riboflavin operon of Bacillus subtilis: unusual symmetric arrangement of the regulatory region. Mol. Gen. Genet. 233, 483–486 (1992).

    CAS  PubMed  Google Scholar 

  45. Edwards, T.E. & Ferré-D'Amaré, 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).

    CAS  PubMed  Google Scholar 

  46. 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).

    CAS  PubMed  Google Scholar 

  47. Mayer, G. & Famulok, M. High-throughput-compatible assay for glmS riboswitch metabolite dependence. ChemBioChem 7, 602–604 (2006).

    CAS  PubMed  Google Scholar 

  48. Blount, K.F., Puskarz, I., Penchovsky, R. & Breaker, R.R. Development and application of a high-throughput assay for glmS riboswitch activators. RNA Biology 3, 77–81 (2006).

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  50. Sudarsan, N., Hammond, M.C., Block, K., Welz, R. & Breaker, R.R. Tandem riboswitch architectures exhibit complex gene control functions. Science 314, 300–304 (2006).

    CAS  PubMed  Google Scholar 

  51. Lee, J.-M. et al. RNA expression analysis using an antisense Bacillus subtilis genome array. J. Bacteriol. 183, 7371–7380 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  52. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

  53. Bacher, A., Eberhardt, S., Fischer, M., Kis, K. & Richter, G. Biosynthesis of vitamin B2 (riboflavin). Annu. Rev. Nutr. 20, 153–167 (2000).

    CAS  PubMed  Google Scholar 

  54. Wickiser, J.K., Winkler, W.C., Breaker, R.R. & Crothers, D.M. The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Mol. Cell 18, 49–60 (2005).

    CAS  PubMed  Google Scholar 

  55. Wickiser, J.K., Cheah, M.T., Breaker, R.R. & Crothers, D.M. The kinetics of ligand binding by an adenine-sensing riboswitch. Biochemistry 44, 13404–13414 (2005).

    CAS  PubMed  Google Scholar 

  56. Koedam, J.C. The mode of action of pyrithiamine as an inducer of thiamine deficiency. Biochim. Biophys. Acta 29, 333–344 (1958).

    CAS  PubMed  Google Scholar 

  57. Di Girolamo, M., Di Girolamo, A., Cini, C., Coccia, R. & De Marco, C. Thialysine utilization for protein synthesis by CHO cells. Physiol. Chem. Phys. Med. NMR 18, 159–164 (1986).

    CAS  PubMed  Google Scholar 

  58. Saxild, H.H. & Nygaard, P. Genetic and physiological characterization of Bacillus subtilis mutants resistant to purine analogs. J. Bacteriol. 169, 2977–2983 (1987).

    CAS  PubMed  PubMed Central  Google Scholar 

  59. Haas, A.L., Laun, N.P. & Begley, T.P. Thi20, a remarkable enzyme from Saccharomyces cerevisiae with dual thiamine biosynthetic and degradation activities. Bioorg. Chem. 33, 338–344 (2005).

    CAS  PubMed  Google Scholar 

  60. McDaniel, B.A., Grundy, F.J., Kurlekar, V.P., Tomsic, J. & Henkin, T.M. Identification of a mutation in the Bacillus subtilis S-adenosylmethionine synthetase gene that results in derepression of S-box gene expression. J. Bacteriol. 188, 3674–3681 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  61. Barrick, J.E. et al. New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc. Natl. Acad. Sci. USA 101, 6421–6426 (2004).

    CAS  PubMed  Google Scholar 

  62. Corbino, K.A. et al. Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria. Genome Biol. 6, R70.1–R70.10 (2005).

    Google Scholar 

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

    CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. Department of Molecular, Cellular and Developmental Biology, Yale University, 266 Whitney Avenue, New Haven, 06520, Connecticut, USA

    Kenneth F Blount & Ronald R Breaker

  2. Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, 06520, Connecticut, USA

    Ronald R Breaker

  3. Howard Hughes Medical Institute, Yale University, 266 Whitney Avenue, New Haven, 06520, Connecticut, USA

    Ronald R Breaker

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  1. Kenneth F Blount
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Correspondence to Kenneth F Blount or Ronald R Breaker.

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K.F.B. and R.R.B. are cofounders of BioRelix, a company that is pursuing intellectual property related to the use of riboswitches as drug targets.

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Blount, K., Breaker, R. Riboswitches as antibacterial drug targets. Nat Biotechnol 24, 1558–1564 (2006). https://doi.org/10.1038/nbt1268

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