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Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea

Nature Chemical Biology volume 6, pages 277282 (2010) | Download Citation

Abstract

A modified base at the first (wobble) position of some tRNA anticodons is critical for deciphering the genetic code. In eukaryotes and eubacteria, AUA codons are decoded by tRNAsIle with modified bases pseudouridine (and/or inosine) and lysidine, respectively. The mechanism by which archaeal species translate AUA codons is unclear. We describe a polyamine-conjugated modified base, 2-agmatinylcytidine (agm2C or agmatidine), at the wobble position of archaeal tRNAIle that decodes AUA codons specifically. We demonstrate that archaeal cells use agmatine to synthesize agm2C of tRNAIle. We also identified a new enzyme, tRNAIle-agm2C synthetase (TiaS), that catalyzes agm2C formation in the presence of agmatine and ATP. Although agm2C is chemically similar to lysidine, TiaS constitutes a distinct class of enzyme from tRNAIle-lysidine synthetase (TilS), suggesting that the decoding systems evolved convergently across domains.

  • Compound C9H12N2O6

    Pseudouridine

  • Compound C10H12N4O5

    Inosine

  • Compound C15H25N5O6

    Lysidine

  • Compound C14H25N7O4

    Agmatidine

  • Compound C5H14N4

    Agmatine

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References

  1. 1.

    & Modified nucleosides and codon recognition. in tRNA: Structure, Biosynthesis, and Function (eds. Söll, D. & RajBhandary, U.L.) 207–224 (American Society for Microbiology, Washington, DC, 1995).

  2. 2.

    Biosynthesis and function of modified nucleosides. in tRNA: Structure, Biosynthesis, and Function (eds. Söll, D. & RajBhandary, U.L.) 165–205 (American Society for Microbiology, Washington, DC, 1995).

  3. 3.

    Biosynthesis and function of tRNA wobble modifications. in Topics in Current Genetics 24–69 (Springer-Verlag, New York, 2005).

  4. 4.

    Codon–anticodon pairing: the wobble hypothesis. J. Mol. Biol. 19, 548–555 (1966).

  5. 5.

    , , , & The modified wobble base inosine in yeast tRNAIle is a positive determinant for aminoacylation by isoleucyl-tRNA synthetase. Biochemistry 36, 8269–8275 (1997).

  6. 6.

    et al. A novel lysine-substituted nucleoside in the first position of the anticodon of minor isoleucine tRNA from Escherichia coli. J. Biol. Chem. 263, 9261–9267 (1988).

  7. 7.

    et al. Codon and amino-acid specificities of a transfer RNA are both converted by a single post-transcriptional modification. Nature 336, 179–181 (1988).

  8. 8.

    et al. An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA. Mol. Cell 12, 689–698 (2003).

  9. 9.

    et al. molecular mechanism of lysidine synthesis that determines tRNA identity and codon recognition. Mol. Cell 19, 235–246 (2005).

  10. 10.

    et al. Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase. Nature 461, 1144–1148 (2009).

  11. 11.

    & Discovery and characterization of tRNAIle lysidine synthetase (TilS). FEBS Lett. 584, 272–277 (2010).

  12. 12.

    , , & The catalytic flexibility of tRNAIle-lysidine synthetase can generate alternative tRNA substrates for isoleucyl-tRNA synthetase. J. Biol. Chem. 284, 9656–9662 (2009).

  13. 13.

    et al. Posttranscriptional modification of tRNA in thermophilic archaea (Archaebacteria). J. Bacteriol. 173, 3138–3148 (1991).

  14. 14.

    Halobacterium volcanii tRNAs. Identification of 41 tRNAs covering all amino acids, and the sequences of 33 class I tRNAs. J. Biol. Chem. 259, 9461–9471 (1984).

  15. 15.

    et al. Identification and characterization of a tRNA decoding the rare AUA codon in Haloarcula marismortui. RNA 14, 117–126 (2008).

  16. 16.

    et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 36, D480–D484 (2008).

  17. 17.

    , & A genomic perspective on protein families. Science 278, 631–637 (1997).

  18. 18.

    , & The complete set of tRNA species in Nanoarchaeum equitans. FEBS Lett. 579, 2945–2947 (2005).

  19. 19.

    et al. A korarchaeal genome reveals insights into the evolution of the Archaea. Proc. Natl. Acad. Sci. USA 105, 8102–8107 (2008).

  20. 20.

    , , & & RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes. BMC Genomics 9, 470 (2008).

  21. 21.

    & Polyamines and abiotic stress: recent advances. Amino Acids 34, 35–45 (2008).

  22. 22.

    , , , & Stabilization of nucleic acids by unusual polyamines produced by an extreme thermophile, Thermus thermophilus. Biochem. J. 388, 427–433 (2005).

  23. 23.

    & Polyamines in microorganisms. Microbiol. Rev. 49, 81–99 (1985).

  24. 24.

    , , & Agmatine is essential for the cell growth of Thermococcus kodakaraensis. FEMS Microbiol. Lett. 287, 113–120 (2008).

  25. 25.

    , , , & Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions. Mol. Cell 21, 97–108 (2006).

  26. 26.

    , , & Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic phenylalanine tRNA. EMBO J. 25, 2142–2154 (2006).

  27. 27.

    , , , & Mass spectrometric identification and characterization of RNA-modifying enzymes. Methods Enzymol. 425, 211–229 (2007).

  28. 28.

    , , & Sulfolobus: a new genus of sulfur-oxidizing bacteria living at low pH and high temperature. Arch. Mikrobiol. 84, 54–68 (1972).

  29. 29.

    et al. Characterization of a Methanosarcina acetivorans mutant unable to translate UAG as pyrrolysine. Mol. Microbiol. 59, 56–66 (2006).

  30. 30.

    , , & Selection of tRNA by the ribosome requires a transition from an open to a closed form. Cell 111, 721–732 (2002).

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Acknowledgements

We are grateful to Y. Sakaguchi, T. Saigo, K. Nishikawa, S. Ohno and Y. Nomura for technical support and many fruitful discussions. Special thanks are due to Thermo Fischer Scientific for FT-MS analysis. This work was supported by Grants-in-Aid for Scientific Research on Priority Areas from the Ministry of Education, Science, Sports, and Culture of Japan (to Tsutomu Suzuki, T.Y. and T.W.); by a Japan Society for the Promotion of Science Fellowship for Japanese Junior Scientists (to Y.I.); by a PRESTO program grant from Japan Science and Technology (to T.N.) and by a grant from the New Energy and Industrial Technology Development Organization (NEDO) (to Tsutomu Suzuki).

Author information

Affiliations

  1. Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan.

    • Yoshiho Ikeuchi
    • , Satoshi Kimura
    • , Takeo Suzuki
    •  & Tsutomu Suzuki
  2. Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan.

    • Tomoyuki Numata
  3. Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Saitama, Japan.

    • Tomoyuki Numata
  4. Department of Biomolecular Science, Faculty of Engineering, Gifu University, Gifu, Japan.

    • Daigo Nakamura
    •  & Takashi Yokogawa
  5. Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan.

    • Toshihiko Ogata
    •  & Takeshi Wada

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Contributions

Y.I. determined the chemical structure of agm2C. S.K. performed biochemical studies of agm2C and TiaS. Takeo Suzuki performed in vivo labeling of agm2C. T.N. performed expression and purification of TiaS. D.N. purified native tRNA under the supervision of T.Y. T.O. supported chemical synthesis of agm2C under the supervision of T.W. All authors discussed the results and commented on the manuscript. Tsutomu Suzuki designed and supervised all the work.

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The authors declare no competing financial interests.

Corresponding author

Correspondence to Tsutomu Suzuki.

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DOI

https://doi.org/10.1038/nchembio.323

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