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Evolution and RNA Relics. A Systems Biology View

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Abstract

The genetic code has evolved from its initial non-degenerate wobble version until reaching its present state of degeneracy. By using the stereochemical hypothesis, we revisit the problem of codon assignations to the synonymy classes of amino-acids. We obtain these classes with a simple classifier based on physico-chemical properties of nucleic bases, like hydrophobicity and molecular weight. Then we propose simple RNA (or more generally XNA, with X for D, P or R) ring structures that present, overlap included, one and only one codon by synonymy class as solutions of a combinatory variational problem. We compare these solutions to sequences of present RNAs considered as relics, with a high interspecific invariance, like invariant parts of tRNAs and micro-RNAs. We conclude by emphasizing some optimal properties of the genetic code.

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Notes

  1. http://felix.unife.it/Root/d-Biology/d-Genetics-and-evolution/d-tRNA-sequences/t-tRNA-compilation, Compilation of tRNA and tRNA Gene Sequences, 1993.

  2. http://helix.nih.gov/docs/online/mfold/node5.html

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Acknowledgements

We are very indebted to C. de Duve, M. Eigen, J. Maynard-Smith (died in 2004), A. Pacault and J. Tonnelat (both died in 2008), for their marvellous books, and also to F. Kepes for fruitful discussions.

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Authors and Affiliations

  1. TIMC-IMAG, UMR CNRS 5525, Faculty of Medicine of Grenoble, University J. Fourier, 38 700, La Tronche, France

    Jacques Demongeot, Nicolas Glade & Andrés Moreira

  2. Institut Universitaire de France, Paris, France

    Jacques Demongeot

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  1. Jacques Demongeot
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Correspondence to Jacques Demongeot.

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Demongeot, J., Glade, N. & Moreira, A. Evolution and RNA Relics. A Systems Biology View. Acta Biotheor 56, 5–25 (2008). https://doi.org/10.1007/s10441-008-9028-y

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