A novel approach for predicting the evolutionary origin of acquisition of foreign genes in bacteria: application of codon usage analyses

Abstract

Lysogenic bacteriophages, are considered as a major player for the introduction of foreign genes into bacterial strains. At the time of introduction foreign genes do not fit well into the translation system of the recipient host bacterium as they tend to retain the characteristics of the donor bacteriophages from which it has been transferred. Consequently foreign genes are poorly transcribed at the early phase of their evolution within the host bacterium. This is largely due to the difference in the codon usage pattern between the horizontally transferred genes and the host bacterium. In this study we present detail analyses of various parameters of the codon usages such as codon adaptation index (CAI), mean difference (MD) of the relative adaptiveness, synonymous substitution rate (SSR) of six different phage encoded toxin genes (cholera toxin, shiga toxin, diphtheria toxin, neurotoxin C1, enterotoxin type A and cytotoxin) and proposed conceptual relationship between the evolutionary time of acquisition of the foreign genes and the selected set of parameters of the codon usage. On the basis of the observed data we hypothesize that CAI, MD and SSR of the phage encoded toxin genes are correlated with the evolutionary time of their acquisition and developed a novel approach based on the analyses of these parameters, that can be used to predict the evolutionary time of their acquisition by the corresponding host bacterium.