Factors Involved in the Codon Usage Bias Among Different Genes in a Genome, And Among Different Sites Within a Gene

Abstract

In this study we have focused on the codon usage bias in E. coli. In chapter 3, we use the population genetics model and the data available on the protein and mRNA levels of the E. coli genes to understand the pattern of codon usage in different genes with different expression levels and see which measure best explains the codon usage pattern. Besides codon bias, by testing for the over-parametrization of the model, we are able to test for the existence of context dependent mutation. We have also fitted the model for the codon usage patter in the Yeast and also tested for the context dependent mutation in this organism.

In chapter 4, we focus on the first 10-15 codons in the genes of E. coli. Motivated by the fact that in this region we observe two phenomena, reduction in translation efficiency and suppression of mRNA secondary structures, we investigate whether the former is a side effect of selection for the latter. For this matter we have generated a set of synonymous randomized sequences, and then by selecting the ones which show weak secondary structures in the mentioned region, we would be able to test the theory. We will also look at the frequencies of the amino acids in E. coli genes and see whether the selection for weak secondary structures in the translation initiation region could be strong enough to not only affect the codon usage, but also the choice of amino acids. We would also provide information on the correlation between the strength of the mRNA secondary structure in the first 13 codons and the overall translation efficiency of the genes.