Genome Codon Index of Pseudomonas aeruginosa: A Codon Index That Utilizes Whole Genome Sequence Data

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Abstract
Codon usage in bacteria is driven by genomic and/or translational constraints. A new measure of codon usage, the genome codon index (GCI), that compares the codon usage of a particular gene with the average codon usage of the genome, was applied to describe codon usage variation in Pseudomonas aeruginosa PAO1. The genome codon indices of the genes of P. aeruginosa PAO1 were consistently high throughout the genome, indicating a pronounced mutational bias (average GCI: 0.678). Major determinants of GCI were found to be the G + C contents, gene size, and the GC skew between leading (mean GCI 0.661) and lagging strand (0.700). The uniform GCI pattern is interrupted by 15 gene islands in the PAO1 genome with lower GCI values; two of these islands are made up by highly expressed ribosomal protein genes. The GCI profile supports the metabolic versatility and ubiquitous lifestyle of P. aeruginosa. First, the uniformly high GCI of almost all genes irrespective of encoded function facilitates the rapid adaptation of expression levels to diverse habitats and environmental stimuli, and, second, the differential GCI of metabolome and ribosomal proteins uncouples the synthesis of ribosomes from the rapidly changing metabolic demands of the cell.

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