Intragenic codon usage in proteobacteria: Translational selection, IS expansion and genomic shrinkage

This manuscript presents a method to systematically study intragenic variations in codon usage using correspondence analysis and the effective number of codons. The method is applied to >1100 proteobacteria. Codon usage biases (measured as inertia) increases with genome size, the same is true for the percentage of inertia explained by the first axis. It is shown that there is often a relaxed or more uniform codon usage near the gene termini. Ithis is not seen n small genomes, notably those of intracellular organisms like Buchnera aphidicola or Rickettsia prowazekii where translational selection plays less of a role. When genes from E. coli, for which translational selection is well described, are split into low, intermediate and high expression, respectively, it is shown that the intragenic codon usage pattern with more uniform usage at termini exist across all three expression groups. Furthermore, the correspondence analysis reveals a unique pattern in Bordetella pertussis due to IS expansion. This study thus shows that translational selection, genome shrinkage and IS expansion result in characteristic patterns in intragenic codon usage.