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Distinct domains of tRNA synthetase recognize the same base pair

Nature volume 451, pages 90–93 (2008)Cite this article

Abstract

Synthesis of proteins containing errors (mistranslation) is prevented by aminoacyl transfer RNA synthetases through their accurate aminoacylation of cognate tRNAs and their ability to correct occasional errors of aminoacylation by editing reactions1,2,3,4,5. A principal source of mistranslation comes from mistaking glycine or serine for alanine, which can lead to serious cell and animal pathologies, including neurodegeneration3. A single specific G·U base pair (G3·U70) marks a tRNA for aminoacylation by alanyl-tRNA synthetase6,7,8,9. Mistranslation occurs when glycine or serine is joined to the G3·U70-containing tRNAs, and is prevented by the editing activity that clears the mischarged amino acid. Previously it was assumed that the specificity for recognition of tRNAAla for editing was provided by the same structural determinants as used for aminoacylation. Here we show that the editing site of alanyl-tRNA synthetase, as an artificial recombinant fragment, targets mischarged tRNAAla using a structural motif unrelated to that for aminoacylation so that, remarkably, two motifs (one for aminoacylation and one for editing) in the same enzyme independently can provide determinants for tRNAAla recognition. The structural motif for editing is also found naturally in genome-encoded protein fragments that are widely distributed in evolution10,11,12. These also recognize mischarged tRNAAla. Thus, through evolution, three different complexes with the same tRNA can guard against mistaking glycine or serine for alanine.

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Figure 1: Domains of AlaRS and AlaXp and deacylation activity of selected fragments.
Figure 2: AlaRS and its fragments are specific for tRNA Ala and influenced by the G3˙U70 base pair.
Figure 3: Multiple checkpoints of tRNA Ala recognition for prevention of mistranslation.

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References

  1. Beebe, K., Ribas De Pouplana, L. & Schimmel, P. Elucidation of tRNA-dependent editing by a class II tRNA synthetase and significance for cell viability. EMBO J. 22, 668–675 (2003)

    Article  CAS  Google Scholar 

  2. Doring, V. et al. Enlarging the amino acid set of Escherichia coli by infiltration of the valine coding pathway. Science 292, 501–504 (2001)

    Article  ADS  CAS  Google Scholar 

  3. Lee, J. W. et al. Editing-defective tRNA synthetase causes protein misfolding and neurodegeneration. Nature 443, 50–55 (2006)

    Article  ADS  CAS  Google Scholar 

  4. Nangle, L. A., De Crecy Lagard, V., Doring, V. & Schimmel, P. Genetic code ambiguity. Cell viability related to the severity of editing defects in mutant tRNA synthetases. J. Biol. Chem. 277, 45729–45733 (2002)

    Article  CAS  Google Scholar 

  5. Nangle, L. A., Motta, C. M. & Schimmel, P. Global effects of mistranslation from an editing defect in mammalian cells. Chem. Biol. 13, 1091–1100 (2006)

    Article  CAS  Google Scholar 

  6. Hou, Y. M. & Schimmel, P. A simple structural feature is a major determinant of the identity of a transfer RNA. Nature 333, 140–145 (1988)

    Article  ADS  CAS  Google Scholar 

  7. Hou, Y. M. & Schimmel, P. Evidence that a major determinant for the identity of a transfer RNA is conserved in evolution. Biochemistry 28, 6800–6804 (1989)

    Article  CAS  Google Scholar 

  8. McClain, W. H. & Foss, K. Changing the acceptor identity of a transfer RNA by altering nucleotides in a “variable pocket”. Science 241, 1804–1807 (1988)

    Article  ADS  CAS  Google Scholar 

  9. Swairjo, M. A. et al. Alanyl-tRNA synthetase crystal structure and design for acceptor-stem recognition. Mol. Cell 13, 829–841 (2004)

    Article  CAS  Google Scholar 

  10. Ahel, I., Korencic, D., Ibba, M. & Soll, D. Trans-editing of mischarged tRNAs. Proc. Natl Acad. Sci. USA 100, 15422–15427 (2003)

    Article  ADS  CAS  Google Scholar 

  11. An, S. & Musier-Forsyth, K. Trans-editing of Cys-tRNAPro by Haemophilus influenzae YbaK protein. J. Biol. Chem. 279, 42359–42362 (2004)

    Article  CAS  Google Scholar 

  12. An, S. & Musier-Forsyth, K. Cys-tRNAPro editing by Haemophilus influenzae YbaK via a novel synthetasėYbaK tRNA ternary complex. J. Biol. Chem. 280, 34465–34472 (2005)

    Article  CAS  Google Scholar 

  13. Pauling, L. in Festschrift fur Prof. Dr. Arthur Stoll 597–602 (Birkhauser, Basel, 1957)

    Google Scholar 

  14. Tsui, W. C. & Fersht, A. R. Probing the principles of amino acid selection using the alanyl-tRNA synthetase from Escherichia coli . Nucleic Acids Res. 9, 4627–4637 (1981)

    Article  CAS  Google Scholar 

  15. Putney, S. D. et al. Primary structure of a large aminoacyl-tRNA synthetase. Science 213, 1497–1501 (1981)

    Article  ADS  CAS  Google Scholar 

  16. Jasin, M., Regan, L. & Schimmel, P. Modular arrangement of functional domains along the sequence of an aminoacyl tRNA synthetase. Nature 306, 441–447 (1983)

    Article  ADS  CAS  Google Scholar 

  17. Cusack, S. et al. A second class of synthetase structure revealed by X-ray analysis of Escherichia coli seryl-tRNA synthetase at 2.5 Å. Nature 347, 249–255 (1990)

    Article  ADS  CAS  Google Scholar 

  18. Ruff, M. et al. Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp). Science 252, 1682–1689 (1991)

    Article  ADS  CAS  Google Scholar 

  19. Dock-Bregeon, A. et al. Transfer RNA-mediated editing in threonyl-tRNA synthetase. The class II solution to the double discrimination problem. Cell 103, 877–884 (2000)

    Article  CAS  Google Scholar 

  20. Sankaranarayanan, R. et al. Zinc ion mediated amino acid discrimination by threonyl-tRNA synthetase. Nature Struct. Biol. 7, 461–465 (2000)

    Article  CAS  Google Scholar 

  21. Karkhanis, V. A., Boniecki, M. T., Poruri, K. & Martinis, S. A. A viable amino acid editing activity in the leucyl-tRNA synthetase CP1-splicing domain is not required in the yeast mitochondria. J. Biol. Chem. 281, 33217–33225 (2006)

    Article  CAS  Google Scholar 

  22. Roy, H., Ling, J., Irnov, M. & Ibba, M. Post-transfer editing in vitro and in vivo by the β subunit of phenylalanyl-tRNA synthetase. EMBO J. 23, 4639–4648 (2004)

    Article  CAS  Google Scholar 

  23. Schimmel, P. & Ribas de Pouplana, L. Formation of two classes of tRNA synthetases in relation to editing functions and genetic code. Cold Spring Harb. Symp. Quant. Biol. 66, 161–166 (2001)

    Article  CAS  Google Scholar 

  24. Regan, L., Bowie, J. & Schimmel, P. Polypeptide sequences essential for RNA recognition by an enzyme. Science 235, 1651–1653 (1987)

    Article  ADS  CAS  Google Scholar 

  25. Fukunaga, R. & Yokoyama, S. Structure of the AlaX-M trans-editing enzyme from Pyrococcus horikoshii . Acta Crystallogr. D 63, 390–400 (2007)

    Article  CAS  Google Scholar 

  26. Sokabe, M. et al. Molecular basis of alanine discrimination in editing site. Proc. Natl Acad. Sci. USA 102, 11669–11674 (2005)

    Article  ADS  CAS  Google Scholar 

  27. Waas, W. F. & Schimmel, P. Evidence that tRNA synthetase-directed proton transfer stops mistranslation. Biochemistry 46, 12062–12070 (2007)

    Article  CAS  Google Scholar 

  28. Beebe, K., Merriman, E. & Schimmel, P. Structure-specific tRNA determinants for editing a mischarged amino acid. J. Biol. Chem. 278, 45056–45061 (2003)

    Article  CAS  Google Scholar 

  29. Beebe, K. et al. A universal plate format for increased throughput of assays that monitor multiple aminoacyl transfer RNA synthetase activities. Anal. Biochem. 368, 111–121 (2007)

    Article  CAS  Google Scholar 

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Acknowledgements

We thank P. O’Maille for his gift of plasmid pH8GW and M. Sokabe for discussions about the model of the tRNA complex with Pyrococcus horikoshi AlaXp. This work was supported by grants from the National Institutes of Health, the Skaggs Foundation, and the National Foundation for Cancer Research.

Author Contributions K.B., M.M. and E.M. performed experiments and produced all materials. K.B., M.M. and P.S. conceived ideas, designed experiments, and wrote and edited the manuscript. All authors reviewed and approved the final manuscript.

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  1. Kirk Beebe and Marissa Mock: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Molecular Biology and Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA,

    Kirk Beebe, Marissa Mock, Eve Merriman & Paul Schimmel

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  3. Eve Merriman
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  4. Paul Schimmel
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Correspondence to Paul Schimmel.

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Beebe, K., Mock, M., Merriman, E. et al. Distinct domains of tRNA synthetase recognize the same base pair. Nature 451, 90–93 (2008). https://doi.org/10.1038/nature06454

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