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Selection on Codon Usage for Error Minimization at the Protein Level Marco Archetti
 

Summary: Selection on Codon Usage for Error Minimization at the Protein Level
Marco Archetti
DeŽ partement de Biologie, Section Ecologie et Evolution, UniversiteŽ de Fribourg, Chemin du MuseŽ e 10, 1700, Fribourg, Switzerland
Received: 30 September 2003 / Accepted: 12 April 2004 [Reviewing Editor: Dr. Massimo Di Giulio]
Abstract. Given the structure of the genetic code,
synonymous codons differ in their capacity to
minimize the effects of errors due to mutation or
mistranslation. I suggest that this may lead, in pro-
tein-coding genes, to a preference for codons that
minimize the impact of errors at the protein level. I
develop a theoretical measure of error minimization
for each codon, based on amino acid similarity. This
measure is used to calculate the degree of error min-
imization for 82 genes of Drosophila melanogaster and
432 rodent genes and to study its relationship with CG
content, the degree of codon usage bias, and the rate
of nucleotide substitution. I show that (i) Drosophila
and rodent genes tend to prefer codons that minimize
errors; (ii) this cannot be merely the effect of mutation
bias; (iii) the degree of error minimization is corre-

  

Source: Archetti, Marco - Department of Organismic and Evolutionary Biology, Harvard University

 

Collections: Biology and Medicine