Advertisement

Evolution of tRNAs Was Driven by Entropic Forces

  • Marco V. JoséEmail author
  • Gabriel S. Zamudio
  • Sávio Torres de Farías
Chapter

Abstract

A succinct review of the role of tRNA and aminoacyl-tRNA synthetases in the origin of the genetic code is provided. The entropy per each site of tRNA molecules is calculated. An entropy profile is obtained for each type of tRNA. When the average of entropy per site of the tRNAs is calculated according to their synthetases, a mirror symmetry is obtained. We conclude that the two codes for amino-acylation and codon-anticodon interactions arose concomitantly, so that these two codes were originally one and the same.

Notes

Acknowledgments

MVJ was financially supported by PAPIIT-IN224015, UNAM, México.

References

  1. 1.
    De Duve C. The second genetic code. Nature. 1998;333:117–8.CrossRefGoogle Scholar
  2. 2.
    Eriani G, Delarue M, Poch O, Gangloff J, Moras D. Partition of aminoacyl-tRNA synthetases into two classes based on mutually exclusive sets of conserved motifs. Nature. 1990;1990(347):203–6.CrossRefGoogle Scholar
  3. 3.
    Farias ST, Guimarães RC. Aminoacyl-tRNA synthetase classes and groups in prokaryotes. J Theor Biol. 2008;21:221–9.CrossRefGoogle Scholar
  4. 4.
    Farias ST, Rêgo TG, José MV. Evolution of transfer RNA and the origin of the translation system. Front Genet. 2014;5:303. doi: 10.3389/fgene.2014.00303.CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Farias ST, Rêgo T, José MV. Origin and evolution of the Peptidyl transferase center from proto-tRNAs. FEBS Open Bio. 2014;2014(4):175–8.CrossRefGoogle Scholar
  6. 6.
    Farías ST, Rêgo TG, José MV. A proposal of the proteome before the Last Universal Common Ancestor (LUCA). Int J Astrobiol. 2015;15:27–31. doi: 10.1017/S1473550415000464.CrossRefGoogle Scholar
  7. 7.
    Hou YM, Schimmel P. A simple structural feature is a major determinant of the identity of a transfer RNA. Nature. 1988;12:140–5.CrossRefGoogle Scholar
  8. 8.
    José MV, Morgado ER, Guimarães RC, Zamudio GS, Farías ST, Bobadilla JR, Sosa D. Three-Dimensional algebraic models of the tRNA code and the 12 graphs for representing the amino acids. Life. 2014;4:341–73. doi: 10.3390/life4030341.CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    José MV, Zamudio GS, Palacios-Pérez M, Bobadilla JR, Farías ST. Symmetrical and thermodynamic properties of phenotypic graphs of amino acids encoded by the primeval RNY code. Orig Life Evol Biosph. 2015;45:77–83. doi: 10.1007/s11084-015-9427-4.CrossRefPubMedGoogle Scholar
  10. 10.
    Moras D. Structural and functional relationships between aminoacyl-tRNA synthetases. Trends Biochem Sci. 1992;17:159–64.CrossRefPubMedGoogle Scholar
  11. 11.
    Nagel GM, Doolittle RF. Phylogenetic analysis of the aminoacyl-tRNA synthetases. J Mol Evol. 1995;40:487–98.CrossRefPubMedGoogle Scholar
  12. 12.
    Park SJ, Schimmel P. Evidence for interaction of an aminoacyl transfer RNA synthetase with a region important for the identity of its cognate transfer RNA. J Biol Chem. 1998;15:16527–30.Google Scholar
  13. 13.
    Rodin S, Rodin A, Ohno S. The presence of codon-anticodon pairs in the acceptor stem of tRNAs. Proc Natl Acad Sci USA. 1996;93:4537–42.CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Rodin S, Ohno S. Four primordial modes of tRNA-synthetase recognition, determined by the (G, C) operational code. Proc Natl Acad Sci USA. 1997;94:5183–8.CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Schimmel P. An operational RNA code for amino acids and variations in critical nucleotide sequences in evolution. J Mol Evol. 1995;40:531–6.CrossRefPubMedGoogle Scholar
  16. 16.
    Schimmel P. In: Go M, Schimmel P, editors. Tracing biological evolution in protein and gene structures. Amsterdam: Elsevier; 1995. p. 1–10.Google Scholar
  17. 17.
    Schimmel P, Giegé R, Moras D, Yokoyama S. An operational RNA code for amino acids and possible relationship to genetic code. Proc Natl Acad Sci USA. 1993;90:8763–8.CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Schwob E, Söll D. Selection of a ‘minimal’ glutaminyl-tRNA synthetase and the evolution of class I synthetases. EMBO J. 1993;15:5201–8.Google Scholar
  19. 19.
    Steitz TA, Moore PB. RNA, the first macromolecular catalyst: the ribosome is a ribozyme. Trends Biochem Sci. 2003;2003(28):411–8.CrossRefGoogle Scholar
  20. 20.
    Woese CR. The emergence of genetic organization. In: Ponnamperuma C, editor. Exobiology. Amsterdam: North-Holland Publishing Co.; 1972. p. 301–41.Google Scholar
  21. 21.
    Yarus M. RNA–ligand chemistry: a testable source for the genetic code. RNA. 2000;6:475–84.CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Marco V. José
    • 1
    Email author
  • Gabriel S. Zamudio
    • 1
  • Sávio Torres de Farías
    • 2
  1. 1.Theoretical Biology Group, Instituto de Investigaciones BiomédicasUniversidad Nacional Autónoma de MéxicoMexico CityMexico
  2. 2.Centro de Ciencias Exactas y NaturalesUniversidade Federal da ParaíbaJoão PessoaBrazil

Personalised recommendations