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The SMK box is a new SAM-binding RNA for translational regulation of SAM synthetase

Nature Structural & Molecular Biology volume 13, pages 226–233 (2006)Cite this article

Abstract

We have identified the SMK box as a conserved RNA motif in the 5′ untranslated leader region of metK (SAM synthetase) genes in lactic acid bacteria, including Enterococcus, Streptococcus and Lactococcus species. This RNA element bound SAM in vitro, and binding of SAM caused an RNA structural rearrangement that resulted in sequestration of the Shine-Dalgarno (SD) sequence. Mutations that disrupted pairing between the SD region and a sequence complementary to the SD blocked SAM binding, whereas compensatory mutations that restored pairing restored SAM binding. The Enterococcus faecalis SMK box conferred translational repression of a lacZ reporter when cells were grown under conditions where SAM pools are elevated, and mutations that blocked SAM binding resulted in loss of repression, demonstrating that the SMK box is functional in vivo. The SMK box therefore represents a new SAM-binding riboswitch distinct from the previously identified S box RNAs.

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Figure 1: Alignment of SMK box sequences from metK genes in Lactobacillales.
Figure 2: Structural models of the SMK box.
Figure 3: Binding of SAM to SMK box RNAs.
Figure 4: RNase H cleavage analysis of the E. faecalis SMK box RNA.
Figure 5: Structural mapping of the E. faecalis SMK box RNA.
Figure 6: SMK box and S box mechanisms.

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References

  1. Grundy, F.J. & Henkin, T.M. Regulation of gene expression by effectors that bind to RNA. Curr. Opin. Microbiol. 7, 126–131 (2004).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  4. Grundy, F.J. & Henkin, T.M. The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in Gram-positive bacteria. Mol. Microbiol. 30, 737–749 (1998).

    Article  CAS  Google Scholar 

  5. Grundy, F.J. & Henkin, T.M. The T box and S box transcription termination control systems. Front. Biosci. 8, d20–d31 (2003).

    Article  CAS  Google Scholar 

  6. McDaniel, B.A., Grundy, F.J., Artsimovitch, I. & Henkin, T.M. Transcription termination control of the S box system: direct measurement of S-adenosylmethionine by the leader RNA. Proc. Natl. Acad. Sci. USA 100, 3083–3088 (2003).

    Article  CAS  Google Scholar 

  7. 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).

    Article  CAS  Google Scholar 

  8. Winkler, W.C., Nahvi, A., Sudarsen, 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).

    Article  CAS  Google Scholar 

  9. McDaniel, B.A., Grundy, F.J. & Henkin, T.M. A tertiary structural element in S box leader RNAs is required for S-adenosylmethionine-directed transcription termination. Mol. Microbiol. 57, 1008–1021 (2005).

    Article  CAS  Google Scholar 

  10. Rodionov, D.A., Vitreschak, A.G., Mironov, A.A. & Gelfand, M.S. Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems. Nucleic Acids Res. 32, 3340–3353 (2004).

    Article  CAS  Google Scholar 

  11. Grundy, F.J. & Henkin, T.M. Synthesis of serine, glycine, cysteine and methionine. in Bacillus subtilis and Its Closest Relatives: from Genes to Cells (eds. Sonenshein, A.L., Hoch, J.A. & Losick, R.) 245–254 (American Society for Microbiology, Washington, DC, USA 2002).

    Chapter  Google Scholar 

  12. Wabiko, H., Ochi, K., Nguyen, D.M., Allen, E.R. & Freese, E. Genetic mapping and physiological consequences of metE mutations of Bacillus subtilis. J. Bacteriol. 170, 2705–2710 (1988).

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  14. Gagnon, Y.R. et al. Clustering and co-transcription of the Bacillus subtilis genes encoding the aminoacyl-tRNA synthetase genes specific for glutamate and for cysteine and the first gene for cysteine biosynthesis. J. Biol. Chem. 269, 7473–7482 (1994).

    CAS  PubMed  Google Scholar 

  15. Mansilla, M.C., Albanesi, D. & deMendoza, D. Transcriptional control of the sulfur-regulated cysH operon encoding genes involved in L-cysteine biosynthesis in Bacillus subtilis. J. Bacteriol. 182, 5885–5892 (2000).

    Article  CAS  Google Scholar 

  16. Guillouard, I. et al. Identification of Bacillus subtilis CysL, a regulator of the cysJI operon, which encodes sulfite reductase. J. Bacteriol. 184, 4681–4689 (2002).

    Article  CAS  Google Scholar 

  17. Fernandez, M., Kleerebezem, M., Kuipers, O.P., Siezen, R.J. & van Kranenburg, R. Regulation of the metC-cysK operon, involved in sulfur metabolism in Lactococcus lactis. J. Bacteriol. 184, 82–90 (2002).

    Article  CAS  Google Scholar 

  18. Sperandio, B., Polard, P., Ehrlich, S.D., Renault, P. & Guedon, E. Sulfur amino acid metabolism and its control in Lactococcus lactis IL1403. J. Bacteriol. 187, 3762–3778 (2005).

    Article  CAS  Google Scholar 

  19. Shelver, D., Rajagopal, L., Harris, T.O. & Rubens, C.E. MtaR, a regulator of methionine transport, is critical for survival of group B streptococcus in vivo. J. Bacteriol. 185, 6592–6599 (2003).

    Article  CAS  Google Scholar 

  20. Greene, R.C. Biosynthesis of methionine. in Escherichia coli and Salmonella: Cellular and Molecular Biology (eds. Neidhardt, F.C. et al.) 542–560 (American Society for Microbiology, Washington, DC, USA, 1996).

    Google Scholar 

  21. Yousef, M.R., Grundy, F.G. & Henkin, T.M. tRNA requirements for glyQS antitermination: a new twist on tRNA. RNA 9, 1148–1156 (2003).

    Article  CAS  Google Scholar 

  22. Grundy, F.J., Waters, D.A., Allen, S.H. & Henkin, T.M. Regulation of the Bacillus subtilis acetate kinase gene by CcpA. J. Bacteriol. 175, 7348–7355 (1993).

    Article  CAS  Google Scholar 

  23. Donnelly, C.E. & Sonenshein, A.L. Promoter-probe plasmid for Bacillus subtilis. J. Bacteriol. 157, 965–967 (1984).

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Anagnostopoulos, C. & Spizizen, J. Requirements for transformation in Bacillus subtilis. J. Bacteriol. 81, 741–746 (1961).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Miller, J. Experiments in Molecular Genetics. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA, 1972).

    Google Scholar 

  26. Grundy, F.J., Moir, T.R., Haldeman, M.T. & Henkin, T.M. Sequence requirements for terminators and antiterminators in the T box transcription antitermination system: disparity between conservation and functional requirements. Nucleic Acids Res. 30, 1646–1655 (2002).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank S. Tigert for technical assistance. Preliminary sequence data were obtained from The Institute for Genomic Research website at http://www.tigr.org. This work was supported by the US National Institutes of Health (grant GM63615).

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  1. Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, 43210, Ohio, USA

    Ryan T Fuchs, Frank J Grundy & Tina M Henkin

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  1. Ryan T Fuchs
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  2. Frank J Grundy
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Correspondence to Tina M Henkin.

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Supplementary Table 1

Oligonucleotide primers (PDF 13 kb)

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Fuchs, R., Grundy, F. & Henkin, T. The SMK box is a new SAM-binding RNA for translational regulation of SAM synthetase. Nat Struct Mol Biol 13, 226–233 (2006). https://doi.org/10.1038/nsmb1059

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