PECULIARITIES OF codon CONTEXT AND SUBSTITUTION WITHIN STREPTOMYCETE GENOMES

Abstract

Actinobacteria of genus Streptomyces attract great interest of researchers. Their genomes encode cryptic gene clusters for as-yet-unknown antibiotics; heterologous expression of metagenomic libraries in model Streptomyces strains allow to discover new classes of compounds. However, it is crucial to understand the rules that govern codon usage in streptomycete genes, if we are to maximize the chances and level of expression of foreign genes in Streptomyces . In this study we addressed two questions related to codon usage in streptomycete genomes. First, we explored if there are patterns of dicodon usage in Streptomyces . Second, we searched for significant differences in patterns of codon substitution in different families of orthologous genes at different phylogenetic depth and degree of essentiality. To this end, we revealed several codon context rules, which are mainly associated with anomalous frequency of G/C downstream of C-ending codons. We developed a new bioinformatics tool, based on previously described bubble plot approach, allowing matrix-like visualization of codon substitution patterns in the dataset. Using this tool, we show that transcriptional factors of AdpA family carry significant fraction of nonsynonymous substitutions, although changes in its pattern for different actinobacterial orders (and as compared to Streptomycetales ) do not follow simple rules.