A Role for Codon Order in Translation Dynamics

G. Cannarozzi, N. N. Schraudolph, M. Faty (joint first authors), P. v. Rohr, M. T. Friberg, A. C. Roth, G. H. Gonnet, and Y. Barral. A Role for Codon Order in Translation Dynamics. Cell, 141(2):355–367, 16 Apr 2010.

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Abstract

The genetic code is degenerate. Each amino acid is encoded by up to six synonymous codons; the choice between these codons influences gene expression. Here, we show that in coding sequences, once a particular codon has been used, subsequent occurrences of the same amino acid do not use codons randomly, but favor codons that use the same tRNA. The effect is pronounced in rapidly induced genes, involves both frequent and rare codons and diminishes only slowly as a function of the distance between subsequent synonymous codons. Furthermore, we found that in S. cerevisiae codon correlation accelerates translation relative to the translation of synonymous yet anticorrelated sequences. The data suggest that tRNA diffusion away from the ribosome is slower than translation, and that some tRNA channeling takes place at the ribosome. They also establish that the dynamics of translation leave a significant signature at the level of the genome.

BibTeX Entry

@article{CanSchFatetal10,
     author = {Gina Cannarozzi and Nicol N. Schraudolph and Mahamadou
               Faty{~(joint~first~authors)} and Peter von Rohr and
               Markus T. Friberg and Alexander C. Roth and
               Gaston H. Gonnet and Yves Barral},
      title = {\href{http://nic.schraudolph.org/pubs/CanSchFatetal10.pdf}{
               A Role for Codon Order in Translation Dynamics}},
      pages = {355--367},
    journal = {\href{http://www.cell.com}{Cell}},
     volume =  141,
     number =  2,
      month = {16 Apr},
       year =  2010,
       issn = {0092-8674},
        doi = {DOI: 10.1016/j.cell.2010.02.036},
   b2h_type = {Journal Papers},
  b2h_topic = {Bioinformatics},
   abstract = {
  The genetic code is degenerate. Each amino acid is encoded by up
  to six synonymous codons; the choice between these codons influences
  gene expression.  Here, we show that in coding sequences, once a
  particular codon has been used, subsequent occurrences of the
  same amino acid do not use codons randomly, but favor codons that
  use the same tRNA. The effect is pronounced in rapidly induced
  genes, involves both frequent and rare codons and diminishes only
  slowly as a function of the distance between subsequent synonymous
  codons.  Furthermore, we found that in S. cerevisiae codon
  correlation accelerates translation relative to the translation
  of synonymous yet anticorrelated sequences. The data suggest that
  tRNA diffusion away from the ribosome is slower than translation,
  and that some tRNA channeling takes place at the ribosome. They
  also establish that the dynamics of translation leave a significant
  signature at the level of the genome.
}}