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Antibacterial lysine analogs that target lysine riboswitches

Nature Chemical Biology volume 3, pages 44–49 (2007)Cite this article

Abstract

Lysine riboswitches are bacterial RNA structures that sense the concentration of lysine and regulate the expression of lysine biosynthesis and transport genes. Members of this riboswitch class are found in the 5′ untranslated region of messenger RNAs, where they form highly selective receptors for lysine. Lysine binding to the receptor stabilizes an mRNA tertiary structure that, in most cases, causes transcription termination before the adjacent open reading frame can be expressed. A lysine riboswitch conceivably could be targeted for antibacterial therapy by designing new compounds that bind the riboswitch and suppress lysine biosynthesis and transport genes. As a test of this strategy, we have identified several lysine analogs that bind to riboswitches in vitro and inhibit Bacillus subtilis growth, probably through a mechanism of riboswitch-mediated repression of lysine biosynthesis. These results indicate that riboswitches could serve as new classes of antibacterial drug targets.

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Figure 1: The structure and function of the lysC riboswitch from B. subtilis.
Figure 2: Molecular recognition by a lysine riboswitch receptor.
Figure 3: Lysine derivatives inhibit bacterial growth and repress gene expression.
Figure 4: Lysine riboswitch mutations confer resistance to lysine derivatives and deregulate gene control.

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Acknowledgements

The authors wish to thank J. Barrick for determining the consensus sequence and secondary structure for the lysine riboswitch. This work was supported by the US National Institutes of Health and the US Defense Advanced Research Projects Agency (DARPA). Riboswitch discovery science is also supported by the Howard Hughes Medical Institute.

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Author notes

  1. Kenneth F Blount, Joy Xin Wang and Jinsoo Lim: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Molecular, Cellular and Developmental Biology, Yale University, 266 Whitney Avenue, KBT 506, New Haven, 06520, Connecticut, USA

    Kenneth F Blount, Joy Xin Wang, Jinsoo Lim, Narasimhan Sudarsan & Ronald R Breaker

  2. Howard Hughes Medical Institute, Yale University, 266 Whitney Avenue, KBT 506, New Haven, 06520, Connecticut, USA

    Joy Xin Wang & Ronald R Breaker

  3. Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, KBT 506, New Haven, 06520, Connecticut, USA

    Ronald R Breaker

Authors
  1. Kenneth F Blount
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  4. Narasimhan Sudarsan
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  5. Ronald R Breaker
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Contributions

K.F.B. and R.R.B. coordinated project plans, execution and preparation of the manuscript. J.L. conducted chemical design and synthesis work. J.X.W. carried out in vitro biochemical analyses of the compounds. J.X.W. and J.L. conducted in vivo expression reporter assays. K.F.B., J.X.W. and N.S. conducted experiments to assess the antibiotic action of the compounds.

Corresponding author

Correspondence to Ronald R Breaker.

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Competing interests

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.

Supplementary information

Supplementary Fig. 1

The consensus and secondary structure for lysine riboswitches. (PDF 413 kb)

Supplementary Fig. 2

The pathways for lysine biosynthesis and import in bacteria. (PDF 772 kb)

Supplementary Fig. 3

Growth of Bacillus subtilis lysine auxotroph strain 1A40 with supplementation of minimal media with various lysine analogs. (PDF 251 kb)

Supplementary Table 1

The distribution of lysine riboswitches among bacterial species. (PDF 554 kb)

Supplementary Table 2

Sporulation efficiency of B. subtilis when grown in the presence of various lysine analogs. (PDF 329 kb)

Supplementary Methods (PDF 143 kb)

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Blount, K., Wang, J., Lim, J. et al. Antibacterial lysine analogs that target lysine riboswitches. Nat Chem Biol 3, 44–49 (2007). https://doi.org/10.1038/nchembio842

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