The relationship between palindrome avoidance and intragenic codon usage variations: a Monte Carlo study.

Several studies have shown that codon usage within genes varies, as it seems dependent on both codon context and codon position within the gene. Given that palindromes in addition often are avoided in genomes, this study aimed at finding out if intragenic variations in codon usage may be a way to control the amount and location of palindromes. A Monte Carlo algorithm was written which resampled the codons in genes while keeping the amino acid sequence of the translation product constant. On the resampled sequences, palindromes were counted and their intragenic positions mapped. Escherichia coli K12 uses type II restriction-modification systems and displays pronounced codon usage phenomena. Using this as a reference organism it was clearly shown that the number of palindromes in genes is generally lower than the amount of palindromes in resampled genes; thus, the succession of codons seems to be a way to decrease the number of palindromes. The intragenic position of palindromes in resampled sequences, however, was largely equal to the position in the native genes, so codon usage phenomena are unlikely to be a way to control the intragenic position of palindromes. The analysis was repeated on two bacteriophages and gave similar same results, even though the virus genomes are much smaller. Studies on the endosymbionts Buchnera sp. APS and Wigglesworthia sp., which seemingly have no type II restriction-modification systems, showed that in these species there is only weak evidence for codon usage acting to control the number of palindromes.