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Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5′- and 3′-halves

Nature volume 433, pages 537–541 (2005)Cite this article

Abstract

Analysis of the genome sequence of the small hyperthermophilic archaeal parasite Nanoarchaeum equitans1,2 has not revealed genes encoding the glutamate, histidine, tryptophan and initiator methionine transfer RNA species. Here we develop a computational approach to genome analysis that searches for widely separated genes encoding tRNA halves that, on the basis of structural prediction, could form intact tRNA molecules. A search of the N. equitans genome reveals nine genes that encode tRNA halves; together they account for the missing tRNA genes. The tRNA sequences are split after the anticodon-adjacent position 37, the normal location of tRNA introns. The terminal sequences can be accommodated in an intervening sequence that includes a 12–14-nucleotide GC-rich RNA duplex between the end of the 5′ tRNA half and the beginning of the 3′ tRNA half. Reverse transcriptase polymerase chain reaction and aminoacylation experiments of N. equitans tRNA demonstrated maturation to full-size tRNA and acceptor activity of the tRNAHis and tRNAGlu species predicted in silico. As the joining mechanism possibly involves tRNA trans-splicing, the presence of an intron might have been required for early tRNA synthesis.

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Figure 1: Predicted split N. equitans tRNA genes.
Figure 2: RT–PCR amplification of the newly identified tRNAs in N. equitans.
Figure 3: Aminoacylation of unfractioned N. equitans tRNA by N. equitans glutamyl-tRNA synthetase and histidyl-tRNA synthetase.
Figure 4: Schematic representation of a 5′ tRNA half gene (tRNAGlu) and the corresponding 3′ tRNA half gene found in N. equitans.

References

  1. Huber, H. et al. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417, 63–67 (2002)

    Article  ADS  CAS  Google Scholar 

  2. Waters, E. et al. The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc. Natl Acad. Sci. USA 100, 12984–12988 (2003)

    Article  ADS  CAS  Google Scholar 

  3. Di Giulio, M. The non-monophyletic origin of the tRNA molecule. J. Theor. Biol. 197, 403–414 (1999)

    Article  CAS  Google Scholar 

  4. Tanaka, T. & Kikuchi, Y. Origin of the cloverleaf shape of transfer RNA—the double-hairpin model: Implication for the role of tRNA intron and the long extra loop. Viva Origino 29, 134–142 (2001)

    CAS  Google Scholar 

  5. Boucher, Y. & Doolittle, W. F. Something new under the sea. Nature 417, 27–28 (2002)

    Article  ADS  CAS  Google Scholar 

  6. Marck, C. & Grosjean, H. tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features. RNA 8, 1189–1232 (2002)

    Article  CAS  Google Scholar 

  7. Eddy, S. R. & Durbin, R. RNA sequence analysis using covariance models. Nucleic Acids Res. 22, 2079–2088 (1994)

    Article  CAS  Google Scholar 

  8. Lowe, T. M. & Eddy, S. R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955–964 (1997)

    Article  CAS  Google Scholar 

  9. Marck, C. & Grosjean, H. Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: evolutionary implications. RNA 9, 1516–1531 (2003)

    Article  CAS  Google Scholar 

  10. Hain, J., Reiter, W. D., Hudepohl, U. & Zillig, W. Elements of an archaeal promoter defined by mutational analysis. Nucleic Acids Res. 20, 5423–5428 (1992)

    Article  CAS  Google Scholar 

  11. Connolly, S. A., Rosen, A. E., Musier-Forsyth, K. & Francklyn, C. S. G-1:C73 recognition by an arginine cluster in the active site of Escherichia coli histidyl-tRNA synthetase. Biochemistry 43, 962–969 (2004)

    Article  CAS  Google Scholar 

  12. Sekine, S. et al. Major identity determinants in the ‘augmented D helix’ of tRNA(Glu) from Escherichia coli . J. Mol. Biol. 256, 685–700 (1996)

    Article  CAS  Google Scholar 

  13. Schurer, H., Schiffer, S., Marchfelder, A. & Mörl, M. This is the end: processing, editing and repair at the tRNA 3′-terminus. Biol. Chem. 382, 1147–1156 (2001)

    CAS  PubMed  Google Scholar 

  14. Xiong, Y., Li, F., Wang, J., Weiner, A. M. & Steitz, T. A. Crystal structures of an archaeal class I CCA-adding enzyme and its nucleotide complexes. Mol. Cell 12, 1165–1172 (2003)

    Article  CAS  Google Scholar 

  15. Lohan, A. J. & Gray, M. W. Methods for analysis of mitochondrial tRNA editing in Acanthamoeba castellanii . Methods Mol. Biol. 265, 315–332 (2004)

    CAS  PubMed  Google Scholar 

  16. Varshney, U., Lee, C. P. & RajBhandary, U. L. Direct analysis of aminoacylation levels of tRNAs in vivo. Application to studying recognition of Escherichia coli initiator tRNA mutants by glutaminyl-tRNA synthetase. J. Biol. Chem. 266, 24712–24718 (1991)

    CAS  PubMed  Google Scholar 

  17. Konarska, M. M., Padgett, R. A. & Sharp, P. A. Trans splicing of mRNA precursors in vitro . Cell 42, 165–171 (1985)

    Article  CAS  Google Scholar 

  18. Solnick, D. Does trans splicing in vitro require base pairing between RNAs? Cell 44, 211 (1986)

    Article  CAS  Google Scholar 

  19. Wissinger, B., Schuster, W. & Brennicke, A. Trans splicing in Oenothera mitochondria: nad1 mRNAs are edited in exon and trans-splicing group II intron sequences. Cell 65, 473–482 (1991)

    Article  CAS  Google Scholar 

  20. Abelson, J., Trotta, C. R. & Li, H. tRNA splicing. J. Biol. Chem. 273, 12685–12688 (1998)

    Article  CAS  Google Scholar 

  21. Fabbri, S. et al. Conservation of substrate recognition mechanisms by tRNA splicing endonucleases. Science 280, 284–286 (1998)

    Article  ADS  CAS  Google Scholar 

  22. Li, H. & Abelson, J. Crystal structure of a dimeric archaeal splicing endonuclease. J. Mol. Biol. 302, 639–648 (2000)

    Article  CAS  Google Scholar 

  23. Kleman-Leyer, K., Armbruster, D. W. & Daniels, C. J. Properties of H. volcanii tRNA intron endonuclease reveal a relationship between the archaeal and eucaryal tRNA intron processing systems. Cell 89, 839–847 (1997)

    Article  CAS  Google Scholar 

  24. Salgia, S. R., Singh, S. K., Gurha, P. & Gupta, R. Two reactions of Haloferax volcanii RNA splicing enzymes: joining of exons and circularization of introns. RNA 9, 319–330 (2003)

    Article  CAS  Google Scholar 

  25. Maizels, N. & Weiner, A. M. Phylogeny from function: evidence from the molecular fossil record that tRNA originated in replication, not translation. Proc. Natl Acad. Sci. USA 91, 6729–6734 (1994)

    Article  ADS  CAS  Google Scholar 

  26. Nagaswamy, U. & Fox, G. E. RNA ligation and the origin of tRNA. Orig. Life Evol. Biosph. 33, 199–209 (2003)

    Article  ADS  CAS  Google Scholar 

  27. Gopalan, V., Vioque, A. & Altman, S. RNase P: variations and uses. J. Biol. Chem. 277, 6759–6762 (2002)

    Article  CAS  Google Scholar 

  28. Schneider, T. D., Stormo, G. D., Gold, L. & Ehrenfeucht, A. Information content of binding sites on nucleotide sequences. J. Mol. Biol. 188, 415–431 (1986)

    Article  CAS  Google Scholar 

  29. Curnow, A. W., Tumbula, D. L., Pelaschier, J. T., Min, B. & Söll, D. Glutamyl-tRNAGln amidotransferase in Deinococcus radiodurans may be confined to asparagine biosynthesis. Proc. Natl Acad. Sci. USA 95, 12838–12843 (1998)

    Article  ADS  CAS  Google Scholar 

  30. Williams, M. A., Johzuka, Y. & Mulligan, R. M. Addition of non-genomically encoded nucleotides to the 3′-terminus of maize mitochondrial mRNAs: truncated rps12 mRNAs frequently terminate with CCA. Nucleic Acids Res. 28, 4444–4451 (2000)

    Article  CAS  Google Scholar 

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Acknowledgements

We thank H. Huber and K. O. Stetter for advice and spirited discussions, M. Thomm for the use of laboratory facilities, and J. Yuan and J. Sabina for critically reading the manuscript. This work was supported by grants from the National Institute of General Medical Sciences and the Department of Energy (to D.S.) and by the German Federal Ministry of Education and Research (BMBF) for the Bioinformatics Competence Center ‘Intergenomics’ (to D.J.).

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Authors and Affiliations

  1. Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, Connecticut, 06520-8114, New Haven, USA

    Lennart Randau, Michael J. Hohn & Dieter Söll

  2. Institut für Mikrobiologie, Technical University Braunschweig, P.O. Box 3329, D-38023, Braunschweig, Germany

    Lennart Randau, Richard Münch & Dieter Jahn

  3. Lehrstuhl für Mikrobiologie und Archaeenzentrum, Universität Regensburg, Universitätsstrasse 31, D-93053, Regensburg, Germany

    Michael J. Hohn

  4. Department of Chemistry, Yale University, 266 Whitney Avenue, Connecticut, 06520-8114, New Haven, USA

    Dieter Söll

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Correspondence to Dieter Söll.

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Randau, L., Münch, R., Hohn, M. et al. Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5′- and 3′-halves. Nature 433, 537–541 (2005). https://doi.org/10.1038/nature03233

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