Does the speed of the ribosome correlate with mathematical properties of the genetic code?

Ivo Wolf

Institute for Medical Informatics
University of Applied Sciences, Mannheim, Germany

Ribosome profiling [1] is a relatively new technique that allows measuring a correlate of the average dwell time of the ribosome at the codons of mRNA strands with sub-codon resolution. Variations of the density of ribosome footprint counts represent differences in the speed of the ribosome [2].

In this talk we will present initial results on the question whether the speed of the ribosome correlates with mathematical properties of the genetic code, as those arising from recent mathematical models of the genetic code [3,4] and the theory of maximal self-complementary circular codes [5].

REFERENCES

  1. N.T. Ingolia, S. Ghaemmaghami, J.R.S. Newman, J.S. Weissman: Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling, Science 324 (5924): 218-223, 2009
  2. N.T. Ingolia, L.F. Lareau, J.S. Weissman: Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes, Cell 147: 789-802, 2011
  3. D.L. Gonzalez, S. Giannerini, R. Rosa: Strong short-range correlations and dichotomic codon classes in coding DNA sequences, Phys Rev E Stat Nonlin Soft Matter Phys. 78(5 Pt 1):051918, 2008
  4. E. Fimmel, A. Danielli, L. Strüngmann: On dichotomic classes and bijections of the genetic code, J.Theor.Biol.(2013), http://dx.doi.org/10.1016/j.jtbi.2013.07.027
  5. D.G. Arquès and C.J. Michel: A Complementary Circular Code in the Protein Coding Genes, J. Theoret. Biol. 182:45–58, 1996