Abstract
In every kingdom of life, GC->AT transitions occur more frequently than any other type of mutation due to the spontaneous deamination of cytidine. In eukaryotic genomes, this slow loss of GC base pairs is counteracted by biased gene conversion which increases genomic GC content as part of the recombination process. However, this type of biased gene conversion has not been observed in bacterial genomes, so we hypothesized that GC->AT transitions cause a reduction of genomic GC content in prokaryotic genomes on an evolutionary time scale. To test this hypothesis, we used a phylogenetic approach to analyze triplets of closely related genomes representing a wide range of the bacterial kingdom. The resulting data indicate that genomic GC content is drifting downward in bacterial genomes where GC base pairs comprise 40% or more of the total genome. In contrast, genomes containing less than 40% GC base pairs have fewer opportunities for GC->AT transitions to occur so genomic GC content is relatively stable or actually increasing. It should be noted that this observed change in genomic GC content is the net change in shared parts of the genome and does not apply to parts of the genome that have been lost or acquired since the genomes being compared shared common ancestor. However, a more detailed analysis of two Caulobacter genomes revealed that the acquisition of mobile elements by the two genomes actually reduced the total genomic GC content as well.
Highlights
Bacterial genomic GC content varies from less than 15% to more than 75% [1]
We found that GC base pairs to AT base pairs (GC->AT) changes were the most common (49% of the 46,043 single nucleotide polymorphisms (SNPs)) while AT->GC SNPs occurred at a frequency of only 21%
In each strain, there has been a net loss of GC base pairs that would have caused a reduction in the genomic GC content of about 0.15% during the time period since their most recent common ancestor (Table 2), which is estimated to have existed 25 million generations ago [19]
Summary
Bacterial genomic GC content varies from less than 15% to more than 75% [1]. a wide range of genomic GC content can be observed among the genera within most bacterial phyla. Biased gene conversion does not appear to occur during recombination events in the high GC genomes of this bacterial species.
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