Prokaryotic Genome Evolution as Assessed by Multivariate Analysis of Codon Usage Patterns

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Abstract
This study analyzed the codon usage patterns in three completely sequenced prokaryotic genomes. The major influences on codon usage biases were identified. It was predicted that most of the as yet unidentified open reading frames will be shown to encode functional proteins. It was also shown that translational selection in Mycoplasma genitalium has been unable to overcome the effects of random genetic drift. The dual influences of mutational pressure and translational selection are at play in the genomes of Haemophilia influenzae and Methanococcus jannaschii. In addition, there is considerable variation in base composition around the genome of M. genitalium, and this variation is gradual. These data support the theory that regional variation in base composition can be attributed to alterations in the dNTP pool during DNA replication.