Journal of Molecular Evolution

, Volume 61, Issue 4, pp 524–530 | Cite as

tRNA Creation by Hairpin Duplication

  • Jeremy Widmann
  • Massimo Di Giulio
  • Michael Yarus
  • Rob KnightEmail author


Many studies have suggested that the modern cloverleaf structure of tRNA may have arisen through duplication of a primordial hairpin, but the timing of this duplication event has been unclear. Here we measure the level of sequence identity between the two halves of each of a large sample of tRNAs and compare this level to that of chimeric tRNAs constructed either within or between groups defined by phylogeny and/or specificity. We find that actual tRNAs have significantly more matches between the two halves than do random sequences that can form the tRNA structure, but there is no difference in the average level of matching between the two halves of an individual tRNA and the average level of matching between the two halves of the chimeric tRNAs in any of the sets we constructed. These results support the hypothesis that the modern tRNA cloverleaf arose from a single hairpin duplication prior to the divergence of modern tRNA specificities and the three domains of life.


tRNA Hairpin duplication Cloverleaf 



This work was supported by a seed grant from the W. M. Keck Foundation RNA Bioinformatics Initiative. We thank members of the Knight and Yarus labs for critical discussion of the manuscript.


  1. Di Giulio M (1995) Was it an ancient gene codifying for a hairpin RNA that, by means of direct duplication, gave rise to the primitive tRNA molecule? J Theor Biol 177:95–101PubMedGoogle Scholar
  2. Di Giulio M (1999) The non-monophyletic origin of the tRNA molecule. J Theor Biol 197:403–414CrossRefPubMedGoogle Scholar
  3. Dick T, Schamel W (1995) Molecular evolution of transfer RNA from two precursor hairpins: implications for the origin of protein synthesis. J Mol Evol 41:1–9CrossRefPubMedGoogle Scholar
  4. Eigen M, Winkler-Oswatitsch R (1981) Transfer-RNA, an early gene? Naturwissenschaften 68:282–292CrossRefPubMedGoogle Scholar
  5. Felsenstein J (1978) Cases in which parsimony and compatibility methods will be positively misleading. Syst Zool 27:401–410Google Scholar
  6. Jukes TH (1995) A comparison of mitochondrial tRNAs in five vertebrates. J Mol Evol 40:537–540PubMedGoogle Scholar
  7. Maizels N, Weiner A. (1994) Phylogeny from function: Evidence from the molecular fossil record that tRNA originated in replication, not translation. Proc Natl Acad Sci USA 91:6729–6734PubMedGoogle Scholar
  8. Nagaswamy U, Fox GE (2003) RNA ligation and the origin of tRNA. Orig Life Evol Biosph 33(2):199–209CrossRefPubMedGoogle Scholar
  9. Nei M, Kumar S, Takahashi K (1998) The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small. Proc Natl Acad Sci USA 95:12390–12397CrossRefPubMedGoogle Scholar
  10. Randau L, Münch R, Hohn M, Jahn D, Söll D (2005) Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5′- and 3′-halves. Nature 433:537–541CrossRefPubMedGoogle Scholar
  11. Saks ME, Sampson JR, Abelson J (1998) Evolution of a transfer RNA gene through a point mutation in the anticodon. Science 279(5357):1665–1670CrossRefPubMedGoogle Scholar
  12. Schimmel P, Henderson B (1994) Possible role of aminoacyl-RNA complexes in noncoded peptide synthesis and origin of coded synthesis. Proc Natl Acad Sci USA 91(24):11283–11286PubMedGoogle Scholar
  13. Sprinzl M, Vassilenko KS (2005) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res 1:33, D139–D140Google Scholar
  14. Tamura K, Schimmel P (2001) Oligonucleotide-directed peptide synthesis in a ribosome- and ribozyme-free system. Proc Natl Acad Sci USA 98:1393–1397CrossRefPubMedGoogle Scholar
  15. Weiner A, Maizels N (1987) tRNA-like structures tag the 3′ ends of genomic RNA molecules for replication: Implications for the origin of protein synthesis. Proc Natl Acad Sci USA 84:7383–7387PubMedGoogle Scholar
  16. Yaniv M, Folk WR, Berg P, Soll L (1974) A single mutational modification of a tryptophan-specific transfer RNA permits aminoacylation by glutamine and translation of the codon UAG. J Mol Biol 86:245–260CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, Inc. 2005

Authors and Affiliations

  • Jeremy Widmann
    • 1
  • Massimo Di Giulio
    • 2
  • Michael Yarus
    • 3
  • Rob Knight
    • 1
    Email author
  1. 1.Department of Chemistry and BiochemistryUniversity of ColoradoBoulderUSA
  2. 2.International Institute of Genetics and BiophysicsCNRItaly
  3. 3.Department of Molecular, Cellular and Developmental BiologyUniversity of ColoradoBoulderUSA

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