The effects of nucleotide bias on genome evolution

Abstract

The genomic G+C content of prokaryotes varies from approximately 23% to 77% among genomes. In contrast, among vertebrates, the variation is greatest within the same genome rather than between genomes. There has been a long-standing controversy concerning the causes of these inter- and intra-specific variations. Is it caused by natural selection, favored by the selectionists or, conversely, is it selectively neutral (the neutralist view)? In this study, we investigated the source of nucleotide compositional variation (nucleotide bias) and the consequences of the bias on protein sequence and genome evolution. Thermal adaptation is a primary example to study the effect of natural selection and has been thoroughly studied in this project. We found that both GC content and length of ribosomal RNA genes show positive correlations with optimal growth temperature in prokaryotes and these correlations are not due to phylogenetic history. The correlations are concentrated almost entirely within the stem regions of the rRNA. The rRNA loops, however, show very constant base composition regardless of temperature optima or genomic GC content. The loops were found to have very high amount of adenosine nucleotides throughout prokaryotes and eukaryotes. These results clearly demonstrated that environmental temperature is a selective force that drives rRNA gene evolution and different segments of the same gene (i.e., the stems and loops of the rRNA gene) experience differential selection, although the mutation spectrum presumably should be similar between the loops and stems. For protein coding genes, mutation and natural selection play a different role compared to the rRNA genes. The neutralist predicts mutational bias would cause protein sequence evolution, while the selectionist would predict that the protein sequence is not related to genomic GC content. To investigate these two postulations and analyze the consequences of nucleotide bias in eukaryotec genomes, we studied homologous genes and their encoded proteins in two flowering plants, Oryza sativa (rice) and Arabidopsis thaliana. While there is a relatively homogenous GC content in the Arabidopsis genes (26% to 69%), the GC content of the rice genes is very heterogeneous (27% to 90%). High GC rice genes encode proteins having a high frequency of GC-rich codons encoded amino acids, i.e., glycine, alanine, arginine and proline. (Abstract shortened by UMI.)