Evidence of Selection upon Genomic GC-Content in Bacteria

• Published in: PLoS genetics Vol. 6; no. 9; p. e1001107
• Main Authors: Hildebrand, Falk, Meyer, Axel, Eyre-Walker, Adam
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.09.2010; Public Library of Science (PLoS)
• Subjects: Bacteria; Bacteria - classification; Bacteria - genetics; Bacterial genetics; Base Composition - genetics; Bias; Binding sites (Biochemistry); Deoxyribonucleic acid; DNA; DNA repair; Evolutionary Biology; Evolutionary Biology/Evolutionary and Comparative Genetics; Evolutionary Biology/Genomics; Evolutionary Biology/Microbial Evolution and Genomics; Gene mutations; Genetics and Genomics; Genetics and Genomics/Comparative Genomics; Genetics and Genomics/Microbial Evolution and Genomics; Genome, Bacterial - genetics; Genomes; Genomics; Hypotheses; Identification and classification; Leprosy; Models, Genetic; Mutation; Mutation - genetics; Phylogenetics; Polymorphism, Single Nucleotide - genetics; Properties; Protein Biosynthesis - genetics; Selection, Genetic; Germany
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1001107

The genomic GC-content of bacteria varies dramatically, from less than 20% to more than 70%. This variation is generally ascribed to differences in the pattern of mutation between bacteria. Here we test this hypothesis by examining patterns of synonymous polymorphism using datasets from 149 bacterial species. We find a large excess of synonymous GC→AT mutations over AT→GC mutations segregating in all but the most AT-rich bacteria, across a broad range of phylogenetically diverse species. We show that the excess of GC→AT mutations is inconsistent with mutation bias, since it would imply that most GC-rich bacteria are declining in GC-content; such a pattern would be unsustainable. We also show that the patterns are probably not due to translational selection or biased gene conversion, because optimal codons tend to be AT-rich, and the excess of GC→AT SNPs is observed in datasets with no evidence of recombination. We therefore conclude that there is selection to increase synonymous GC-content in many species. Since synonymous GC-content is highly correlated to genomic GC-content, we further conclude that there is selection on genomic base composition in many bacteria.