across bacterial phyla, distantly-related genomes with similar genomic gc content have similar patterns of amino acid usage在细菌类群,较为疏远的基因组具有相似基因的氨基酸使用gc含量也有类似的模式.pdfVIP

Across Bacterial Phyla, Distantly-Related Genomes with Similar Genomic GC Content Have Similar Patterns of Amino Acid Usage John Lightfield¤a, Noah R. Fram¤b, Bert Ely* Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America Abstract The GC content of bacterial genomes ranges from 16% to 75% and wide ranges of genomic GC content are observed within many bacterial phyla, including both Gram negative and Gram positive phyla. Thus, divergent genomic GC content has evolved repeatedly in widely separated bacterial taxa. Since genomic GC content influences codon usage, we examined codon usage patterns and predicted protein amino acid content as a function of genomic GC content within eight different phyla or classes of bacteria. We found that similar patterns of codon usage and protein amino acid content have evolved independently in all eight groups of bacteria. For example, in each group, use of amino acids encoded by GC-rich codons increased by approximately 1% for each 10% increase in genomic GC content, while the use of amino acids encoded by AT- rich codons decreased by a similar amount. This consistency within every phylum and class studied led us to conclude that GC content appears to be the primary determinant of the codon and amino acid usage patterns observed in bacterial genomes. These results also indicate that selection for translational efficiency of highly expressed genes is constrained by the genomic parameters associated with the GC content of the host genome. Citation: Lightfield J, Fram NR, Ely B (2011) Across Bacterial Phyla, Distantly-Related Genomes with Similar Genomic GC Content Have Similar Patterns of Amino Acid Usage. PLoS ONE 6(3): e17677. doi:10.1371/journal.pone.0017677 Editor: Michael Otto, National Institutes of Health, United States of America Received Novembe