Modifying the Translation Efficiency: The Role of Codon Pair Biases

Source: Coleman et al (2008). Virus Attenuation by Genome-Scale Changes in Codon Pair Bias. Science 320: 1784-1787.

While there is a huge number of possibilities for two adjacent codons, many of them rarely happen and some of them occur more frequently than predicted by chance alone. This distribution of codon frequencies, in part, can be explained by the amino acid usages in the proteins; however, even synonymous codons show drastically different codon-pair biases. Although the actual mechanism is not known, these biases are believed to affect translation efficiency.

In this paper, the authors use the concept of codon pair biases to synthesize polioviruses with maximum or minimum codon-pair biases. For example, in the min version, for every two amino acids they choose the least frequent codon pair. They subsequentlu show that these altered codon-pair usages drastically affects the virulence of polio virus. These viruses are highly attenuated can be actually used as vaccines to boost the immunity of the tested rats.