Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America.
PLoS One. 2021 May 26;16(5):e0244163. doi: 10.1371/journal.pone.0244163. eCollection 2021.
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.
在生命的每个王国中，由于胞嘧啶的自发脱氨作用，GC->AT 转换比任何其他类型的突变都更频繁地发生。在真核基因组中，这种 GC 碱基对的缓慢丢失被偏向性基因转换所抵消，偏向性基因转换作为重组过程的一部分增加了基因组的 GC 含量。然而，这种类型的偏向性基因转换在细菌基因组中并未观察到，因此我们假设 GC->AT 转换会导致细菌基因组的 GC 含量在进化时间尺度上减少。为了验证这一假设，我们使用系统发育方法分析了代表细菌王国广泛范围的三个密切相关的基因组。所得数据表明，在 GC 碱基对占总基因组 40%或更多的细菌基因组中，基因组 GC 含量呈下降趋势。相比之下，GC 碱基对含量低于 40%的基因组发生 GC->AT 转换的机会较少，因此基因组 GC 含量相对稳定或实际上在增加。应该注意的是，这种观察到的基因组 GC 含量变化是基因组共享部分的净变化，不适用于自比较的基因组具有共同祖先以来丢失或获得的基因组部分。然而，对两个 Caulobacter 基因组的更详细分析表明，这两个基因组实际上通过获得移动元件而降低了总基因组 GC 含量。
