Method to Identify Silent Codon Mutations That May Alter Peptide Elongation Kinetics and Co-translational Protein...

Due to the redundancy of the protein genetic code, mutational changes in the second or third nucleotide of an existing codon may not change the amino acid specification of the resulting modified codon. When peptide primary sequence is unchanged by mutation, that mutation is assumed to have no functional consequences. However, for one key gene involved in drug transport, MDR-1, several silent, synonymous mutations have been shown to alter protein structure and substrate affinity (Kimchi-Sarfaty et al., Science 315:525-528, 2007). The mechanism of these changes, in the absence of primary amino acid sequence changes, appears to be the change in abundance of the transfer RNA molecules complementary to the mutated, although synonymous, new codon. Transfer RNA abundance is proportional to the frequency of each codon as found in human protein coding DNA (Sharp et al., Nucleic Acids Res 14(13):5125-5143, 1986). These frequencies have been mapped for many thousands of human proteins (Nakamura et al., Nucleic Acids Res 28:292, 2000). This method analyzes silent codon mutations in whole genome data. Where there are large changes in codon frequency resulting from codon sequence mutation, the affected proteins are mapped to potential disease pathways, in the context of clinical phenotypes associated with the patient genome data.