Hurst L D, Merchant A R
Department of Biology and Biochemistry, University of Bath, UK.
Proc Biol Sci. 2001 Mar 7;268(1466):493-7. doi: 10.1098/rspb.2000.1397.
The causes of the variation between genomes in their guanine (G) and cytosine (C) content is one of the central issues in evolutionary genomics. The thermal adaptation hypothesis conjectures that, as G:C pairs in DNA are more thermally stable than adenonine:thymine pairs, high GC content may he a selective response to high temperature. A compilation of data on genomic GC content and optimal growth temperature for numerous prokaryotes failed to demonstrate the predicted correlation. By contrast, the GC content of Structural RNAs is higher at high temperatures. The issue that we address here is whether more freely evolving sites in exons (i.e. codonic third positions) evolve in the same manner as genomic DNA as a whole, Showing no correlated response, or like structural RNAs showing a strong correlation. The latter pattern would provide strong support for the thermal adaptation hypothesis, as the variation in GC content between orthologous genes is typically most profoundly seen at codon third sites (GC3). Simple analysis of completely sequenced prokaryotic genomes shows that GC3, but not genomic GC, is higher on average in thermophilic species. This demonstrates, if nothing else, that the results from the two measures cannot be presumed to be the same. A proper analysis, however, requires phylogenetic control. Here, therefore, we report the results of a comparative analysis of GC composition and optimal growth temperature for over 100 prokaryotes. Comparative analysis fails to show, in either Archea or Eubacteria, any hint of connection between optimal growth temperature and GC content in the genome as a whole, in protein-coding regions or, more crucially at GC. Conversely, comparable analysis confirms that GC content of structural RNA is strongly correlated with optimal temperature. Against the expectations of the thermal adaptation hypothesis, within prokaryotes GC content in protein-coding genies, even at relatively freely evolving sites, cannot be considered an adaptation to the thermal environment.
基因组中鸟嘌呤（G）和胞嘧啶（C）含量存在差异的原因是进化基因组学的核心问题之一。热适应假说推测，由于DNA中的G:C碱基对比腺嘌呤:胸腺嘧啶碱基对具有更高的热稳定性，高GC含量可能是对高温的一种选择性反应。对众多原核生物的基因组GC含量和最佳生长温度数据进行汇总后，未能证明存在预期的相关性。相比之下，结构RNA的GC含量在高温下更高。我们在此探讨的问题是，外显子中进化更自由的位点（即密码子的第三位）是与整个基因组DNA的进化方式相同，不显示相关反应，还是与结构RNA一样显示出强烈的相关性。后一种模式将为热适应假说提供有力支持，因为直系同源基因之间GC含量的差异通常在密码子第三位（GC3）最为明显。对完全测序的原核生物基因组进行简单分析表明，嗜热物种的GC3平均水平较高，但基因组GC并非如此。这至少表明，不能假定这两种测量结果相同。然而，进行恰当的分析需要系统发育控制。因此，我们在此报告对100多种原核生物的GC组成和最佳生长温度进行比较分析的结果。比较分析未能在古菌或真细菌中显示出最佳生长温度与整个基因组、蛋白质编码区域（更关键的是GC3）的GC含量之间存在任何关联。相反，类似分析证实结构RNA的GC含量与最佳温度密切相关。与热适应假说的预期相反，在原核生物中，即使在相对进化自由的位点，蛋白质编码基因中的GC含量也不能被视为对热环境的一种适应。
