  Messenger RNA encodes a sequence of amino acids by using codons. For most
amino acids there are multiple synonymous codons that can encode the amino
acid. The translation speed can vary from one codon to another, thus there is
room for changing the ribosome speed while keeping the amino acid sequence and
hence the resulting protein. Recently, it has been noticed that the choice of
the synonymous codon, via the resulting distribution of slow- and
fast-translated codons, affects not only on the average speed of one ribosome
translating the messenger RNA (mRNA) but also might have an effect on nearby
ribosomes by affecting the appearance of "traffic jams" where multiple
ribosomes collide and form queues. To test this "context effect" further, we
here investigate the effect of the sequence of synonymous codons on the
ribosome traffic by using a ribosome traffic model with codon-dependent rates,
estimated from experiments. We compare the ribosome traffic on wild type
sequences and sequences where the synonymous codons were swapped randomly. By
simulating translation of 87 genes, we demonstrate that the wild type
sequences, especially those with a high bias in codon usage, tend to have the
ability to reduce ribosome collisions, hence optimizing the cellular investment
in the translation apparatus. The magnitude of such reduction of the
translation time might have a significant impact on the cellular growth rate
and thereby have importance for the survival of the species.
