Speaker
Alexandre Morozov
Description
Frequencies of synonymous codons (nucleotide triplets in the gene
which are translated into amino acids by the ribosome) are typically
non-uniform, despite the fact that such codons correspond to the same
amino acid in the genetic code. This phenomenon, known as codon
bias, is broadly believed to be due to a combination of factors including
genetic drift, mutational effects, and selection for speed and accuracy
of codon translation; however, quantitative modeling of codon bias has
been elusive. I will present a biophysical model which explains
genome-wide codon frequencies observed across 20 organisms. Our
model implements detailed codon-level treatment of mutations, and
includes two contributions to codon fitness which describe codon
translation speed and accuracy. We find that the observed patterns of
genome-wide codon usage are consistent with a strong selective
penalty for mistranslated amino acids, while the dependence of codon
fitness on translation speed is much weaker on average. Treating the
translation process explicitly in the context of a finite ribosomal pool
has allowed us to estimate mutation rates directly from the gene
sequences. Overall, our approach offers a unified biophysical and
population genetics framework for understanding codon bias.
Primary author
Alexandre Morozov
