Codon Usage Optimization in the Prokaryotic Tree of Life: How Synonymous Codons Are Differentially Selected in Sequence Domains with Different Expression Levels and Degrees of Conservation

Abstract

The prokaryotic genomes—the current heritage of the most ancient life forms on earth—are comprised of diverse gene sets, all characterized by varied origins, ancestries, and spatial-temporal expression patterns. Such genetic diversity has for a long time raised the question of how cells shape their coding strategies to optimize protein demands (i.e., product abundance) and accuracy (i.e., translation fidelity) through the use of the same genetic code in genomes with GC contents that range from less than 20 to more than 80%. Here, we present evidence on how codon usage is adjusted in the prokaryotic tree of life and on how specific biases have operated to improve translation. Through the use of proteome data, we characterized conserved and variable sequence domains in genes of either high or low expression level and quantitated the relative weight of efficiency and accuracy—as well as their interaction—in shaping codon usage in prokaryotes.