Letter | Published:

Domain-specific recruitment of amide amino acids for protein synthesis

Nature volume 407, pages 106110 (07 September 2000) | Download Citation



The formation of aminoacyl-transfer RNA is a crucial step in ensuring the accuracy of protein synthesis. Despite the central importance of this process in all living organisms, it remains unknown how archaea and some bacteria synthesize Asn-tRNA and Gln-tRNA. These amide aminoacyl-tRNAs can be formed by the direct acylation of tRNA, catalysed by asparaginyl-tRNA synthetase and glutaminyl-tRNA synthetase, respectively. A separate, indirect pathway involves the formation of mis-acylated Asp-tRNAAsn or Glu-tRNA Gln, and the subsequent amidation of these amino acids while they are bound to tRNA, which is catalysed by amidotransferases1,2. Here we show that all archaea possess an archaea-specific heterodimeric amidotransferase (encoded by gatD and gatE) for Gln-tRNA formation. However, Asn-tRNA synthesis in archaea is divergent: some archaea use asparaginyl-tRNA synthetase, whereas others use a heterotrimeric amidotransferase (encoded by the gatA, gatB and gatC genes). Because bacteria primarily use transamidation3, and the eukaryal cytoplasm uses glutaminyl-tRNA synthetase, it appears that the three domains use different mechanisms for Gln-tRNA synthesis; as such, this is the only known step in protein synthesis where all three domains have diverged. Closer inspection of the two amidotransferases reveals that each of them recruited a metabolic enzyme to aid its function; this provides direct evidence for a relationship between amino-acid metabolism and protein biosynthesis.

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  1. 1.

    & Transfer RNA as a cofactor coupling synthesis with that of protein. Proc. Natl Acad. Sci. USA 61, 229–236 (1968).

  2. 2.

    , & tRNA-dependent asparagine formation. Nature 382, 589–590 ( 1996).

  3. 3.

    , , & Widespread use of the Glu-tRNAGln transamidation pathway among bacteria. J. Biol. Chem. 271, 14856– 14863 (1996).

  4. 4.

    & in The Enzymes Vol. 10 (ed. Boyer, P.) 489–538 (Academic, New York, 1974).

  5. 5.

    & Codon assignments and fidelity of translation in a cell-free protein-synthesizing system from an extremely halophilic bacterium. Can. J. Biochem. 46, 937–944 (1967).

  6. 6.

    et al. Glu-tRNAGln amidotransferase: a novel heterotrimeric enzyme required for correct decoding of glutamine codons during translation. Proc. Natl Acad. Sci. USA 94, 11819– 11826 (1997).

  7. 7.

    et al. A euryarchaeal lysyl-tRNA synthetase: resemblance to class I synthetases. Science 278, 1119–1122 (1997).

  8. 8.

    , , & Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol. Mol. Biol. Rev. 64, 202–236 (2000).

  9. 9.

    , , & L-asparaginase genes in Escherichia coli: isolation of mutants and characterization of the ansA gene and its protein product. J. Bacteriol. 166, 135–142 (1986).

  10. 10.

    , , , & Glutamyl-tRNAGln amidotransferase in Deinococcus radiodurans may be confined to asparagine biosynthesis. Proc. Natl Acad. Sci. USA 95, 12838–12843 (1998).

  11. 11.

    , , & Evolution of aminoacyl-tRNA synthetases–analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res. 9, 689– 710 (1999).

  12. 12.

    & Thermus thermophilus: a link in evolution of the tRNA-dependent amino acid amidation pathways. Proc. Natl Acad. Sci. USA 95, 12832– 12837 (1998).

  13. 13.

    , , & Protein biosynthesis in organelles requires misaminoacylation of tRNA. Nature 331, 187–190 ( 1988).

  14. 14.

    & Gene descent, duplication, and horizontal transfer in the evolution of glutamyl- and glutaminyl-tRNA synthetases. J. Mol. Evol. 49, 485– 495 (1999).

  15. 15.

    & An attempt to pinpoint the phylogenetic introduction of glutaminyl-tRNA synthetase among bacteria. J. Mol. Evol. 49, 709–715 (1999).

  16. 16.

    , , & Modular evolution of the Glx-tRNA synthetase family: rooting of the evolutionary tree between the bacteria and archaea/eukarya branches. Eur. J. Biochem. 256, 80–87 ( 1998).

  17. 17.

    et al. A nuclear genetic lesion affecting Saccharomyces cerevisiae mitochondrial translation is complemented by a homologous Bacillus gene. J. Bacteriol. 179, 5625– 5627 (1997).

  18. 18.

    , & Leishmania tarentolae contains distinct cytosolic and mitochondrial glutaminyl-tRNA synthetase activities. Proc. Natl Acad. Sci. USA 94, 7903–7908 (1997).

  19. 19.

    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).

  20. 20.

    , , , & Interactions between tRNA identity nucleotides and their recognition sites in glutaminyl-tRNA synthetase determine the cognate amino acid affinity of the enzyme. Proc. Natl Acad. Sci. USA 93, 6953–6958 ( 1996).

  21. 21.

    et al. Recognition of bases in Escherichia coli tRNA Gln by glutaminyl-tRNA synthetase: a complete identity set. EMBO J. 11, 4159–4165 ( 1992).

  22. 22.

    & Gene for yeast glutamine tRNA synthetase encodes a large amino-terminal extension and provides a strong confirmation of the signature sequence for a group of the aminoacyl-tRNA synthetases. J. Biol. Chem. 262, 10801– 10806 (1987).

  23. 23.

    , & Acyl transfer activity of an amidase from Rhodococcus sp. strain R312: formation of a wide range of hydroaxamic acids. Appl. Environ. Microbiol. 64, 2844– 2852 (1998).

  24. 24.

    T.-F. A co-evolution theory of the genetic code. Proc. Natl Acad. Sci. USA 72, 1909–1912 ( 1975).

  25. 25.

    et al. An aminoacyl-tRNA synthetase paralog with a catalytic role in histidine biosynthesis. Proc. Natl Acad. Sci. USA 96, 8985–8990 (1999).

  26. 26.

    Molecular evolution: aminoacyl-tRNA synthetases on the loose. Curr. Biol. 9, R842–R844 (1999).

  27. 27.

    The RNA world, the genetic code and the tRNA molecule. Trends Genet. 16, 17–19 ( 2000).

  28. 28.

    , , & Archaeal-type lysyl-tRNA synthetase in the Lyme disease spirochete Borrelia burgdorferi . Proc. Natl Acad. Sci. USA 94, 14383 –14388 (1997).

  29. 29.

    et al. One polypeptide with two aminoacyl-tRNA synthetase activities. Science 287, 479–482 (2000).

  30. 30.

    et al. Overexpression of archaeal proteins in Escherichia coli. Biotechnol. Lett. 20, 207– 210 (1998).

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We thank R. Hedderich for M. thermoautotrophicum Marburg cells, J. Reeve for M. thermoautotrophicum ΔH DNA, K. O. Stetter for Pyrococcus cells, and H. Kobayashi for E. coli GlnRS and E. coli tRNAGln2 transcript. We also thank M. Ibba for critically reading the manuscript and S. Fitz-Gibbon, T. Hartsch, A. Johann, D. Oesterhelt, A. Ruepp and S. Schuster for sharing unpublished sequence data. D.L.T. and H.D.B. are postdoctoral fellows of the National Institute of General Medical Sciences and the EMBO, respectively. This work was supported by grants from the National Institute of General Medical Sciences.

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    • Debra L. Tumbula
    •  & Hubert D. Becker

    These authors contributed equally to this work


  1. *Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA

    • Debra L. Tumbula
    • , Hubert D. Becker
    • , Wei-zhong Chang
    •  & Dieter Söll
  2. ‡Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA

    • Dieter Söll


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Correspondence to Dieter Söll.

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