Advertisement

A Non-neutral Origin for Error Minimization in the Origin of the Genetic Code

  • Massimo Di Giulio
Letter to the Editor

Abstract

Massey (J Mol Evol 67:510–516, 2008; J Theor Biol 408:237–242, 2016; Nat Comput. https://doi.org/10.1007/s11047-017-9669-3, 2018) claims that the error minimization of the genetic code is derived by means of a neutral process and was not due to the action of natural selection. Here, I argue that this neutralist hypothesis of the origin of error minimization is not based directly on any neutral process but it could be only indirectly. On the contrary, it has been natural selection that has acted during the origin of the genetic code determining the property that similar amino acids are coded by similar codons within the genetic code table.

Keywords

Error minimization Natural selection Genetic code coevolution theory Genetic code physicochemical theory 

References

  1. Crick FHC (1968) The origin of the genetic code. J Mol Biol 38:376–379CrossRefGoogle Scholar
  2. Di Giulio M (1989a) The extension reached by the minimization of the polarity distances during the evolution of the genetic code. J Mol Evol 29:288–293CrossRefGoogle Scholar
  3. Di Giulio M (1989b) Some aspects of the organization and evolution of the genetic code. J Mol Evol 29:191–201CrossRefGoogle Scholar
  4. Di Giulio M (1996) The β-sheets of proteins, the biosynthetic relationships between amino acids, and the origin of the genetic code. Orig Life Evol Biosph 26:589–609CrossRefGoogle Scholar
  5. Di Giulio M (1998) Reflections on the origin of the genetic code: a hypothesis. J Theor Biol 191:191–196CrossRefGoogle Scholar
  6. Di Giulio M (2002) Genetic code origin: are the pathways of type Glu-tRNAGln->Gln-tRNAGln molecular fossils or not? J Mol Evol 55:616–622CrossRefGoogle Scholar
  7. Di Giulio M (2008) An extension of the coevolution theory of the origin of the genetic code. Biol Direct 3:37CrossRefGoogle Scholar
  8. Di Giulio M (2015) A model for the origin of the first mRNAs. J Mol Evol 81:10–17CrossRefGoogle Scholar
  9. Di Giulio M (2016a) An autotrophic origin for the coded amino acids is concordant with the coevolution theory of the genetic code. J Mol Evol 83:93–96CrossRefGoogle Scholar
  10. Di Giulio M (2016b) The lack of foundation in the mechanism on which are based the physico-chemical theories for the origin of the genetic code is counterposed to the credible and natural mechanism suggested by the coevolution theory. J Theor Biol 399:134–140CrossRefGoogle Scholar
  11. Di Giulio M (2017a) Some pungent arguments against the physico-chemical theories of the origin of the genetic code and corroborating the coevolution theory. J Theor Biol 414:1–4CrossRefGoogle Scholar
  12. Di Giulio M (2017b) The aminoacyl-tRNA synthetases had only a marginal role in the origin of the organization of the genetic code: evidence in favor of the coevolution theory. J Theor Biol 432:14–24CrossRefGoogle Scholar
  13. Di Giulio M (2018) A discriminative test among the different theories proposed to explain the origin of the genetic code: the coevolution theory finds additional support. Biosystems 169–170:1–4CrossRefGoogle Scholar
  14. Di Giulio M, Amato U (2009) The close relationship between the biosynthetic families of amino acids and the organisation of the genetic code. Gene 435:9–12CrossRefGoogle Scholar
  15. Di Giulio M, Medugno M (1999) Physicochemical optimization in the genetic code origin as the number of codified amino acids increases. J Mol Evol 49:1–10CrossRefGoogle Scholar
  16. Dillon LS (1973) The origins of the genetic code. Bot Rev 39:301–345CrossRefGoogle Scholar
  17. Epstein CJ (1966) Role of the amino-acid code and of selection for conformation in the evolution of proteins. Nature 210:25–28CrossRefGoogle Scholar
  18. Facchiano A, Di Giulio M (2018) The genetic code is not an optimal code in a model taking into account both the biosynthetic relationships between amino acids and their physicochemical properties. J Theor Biol 459:45–51CrossRefGoogle Scholar
  19. Fitch W, Upper K (1987) The phylogeny of tRNA sequences provides evidence for ambiguity reduction in the origin of the genetic code. Cold Spring Harbor Symp Quant Biol 52:759–767CrossRefGoogle Scholar
  20. Goldberg AL, Wittes RE (1966) Genetic code: aspects of organization. Science 153:420–424CrossRefGoogle Scholar
  21. Higgs PG (2009) A four-column theory for the origin of the genetic code: tracing the evolutionary pathways that gave rise to an optimized code. Biol Direct 4:16CrossRefGoogle Scholar
  22. Massey SE (2008) A neutral origin for error minimization in the genetic code. J Mol Evol 67:510–516CrossRefGoogle Scholar
  23. Massey SE (2016) The neutral emergence of error minimized genetic codes superior to the standard genetic code. J Theor Biol 408:237–242CrossRefGoogle Scholar
  24. Massey SE (2018) How to ‘find’an error minimized genetic code: neutral emergence as an alternative to direct Darwinian selection for evolutionary optimization. Nat Comput.  https://doi.org/10.1007/s11047-017-9669-3 CrossRefGoogle Scholar
  25. Nelsestuen GL (1978) Amino acid-directed nucleic acid synthesis. A possible mechanism in the origin of life. J Mol Evol 11:109–120CrossRefGoogle Scholar
  26. Sjostrom M, Wold SA (1985) A multivariate study of the relationship between the genetic code and the physico-chemical properties of amino acids. J Mol Evol 22:272–277CrossRefGoogle Scholar
  27. Sonneborn TM (1965) Degeneracy of the genetic code: extent, nature, and genetic implications. In: Bryson V, Vogel HJ (eds) Evolving genes and proteins. Academic Press, New YorkGoogle Scholar
  28. Taylor FJR, Coates D (1989) The code within the codons. BioSystems 22:177–187CrossRefGoogle Scholar
  29. van der Gulik PT, Hoff WD (2011) Unassigned codons, nonsense suppression, and anticodon modifications in the evolution of the genetic code. J Mol Evol 73:59–69CrossRefGoogle Scholar
  30. Woese CR (1965) On the evolution of the genetic code. Proc Natl Acad Sci USA 54:1546–1552CrossRefGoogle Scholar
  31. Wolfenden RV, Cullis PM, Southgate CCF (1979) Water, protein folding, and the genetic code. Science 206:575–577CrossRefGoogle Scholar
  32. Wong JT (1975) A co-evolution theory of the genetic code. Proc Natl Acad Sci USA 72:1909–1912CrossRefGoogle Scholar
  33. Wong JT (1980) Role of minimization of chemical distances between amino acids in the evolution of the genetic code. Proc Natl Acad Sci USA 77:1083–1086CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Early Evolution of Life LaboratoryInstitute of Biosciences and Bioresources, CNRNaplesItaly

Personalised recommendations