Higgs Paul G, Ran Wenqi
Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada.
Mol Biol Evol. 2008 Nov;25(11):2279-91. doi: 10.1093/molbev/msn173. Epub 2008 Aug 6.
The typical number of tRNA genes in bacterial genomes is around 50, but this number varies from under 30 to over 120. We argue that tRNA gene copy numbers evolve in response to translational selection. In rapidly multiplying organisms, the time spent in translation is a limiting factor in cell division; hence, it pays to duplicate tRNA genes, thereby increasing the concentration of tRNA molecules in the cell and speeding up translation. In slowly multiplying organisms, translation time is not a limiting factor, so the overall translational cost is minimized by reducing the tRNAs to only one copy of each required gene. Translational selection also causes a preference for codons that are most rapidly translated by the current tRNAs; hence, codon usage and tRNA gene content will coevolve to a state where each is adapted to the other. We show that there is often more than one stable coevolved state. This explains why different combinations of tRNAs and codon bias can exist for different amino acids in the same organism. We analyze a set of 80 complete bacterial genomes and show that the theory predicts many of the trends that are seen in these data.
细菌基因组中tRNA基因的典型数量约为50个，但这个数量在30以下到120以上之间变化。我们认为tRNA基因拷贝数是响应翻译选择而进化的。在快速繁殖的生物体中，用于翻译的时间是细胞分裂的一个限制因素；因此，复制tRNA基因是有好处的，从而增加细胞中tRNA分子的浓度并加快翻译速度。在繁殖缓慢的生物体中，翻译时间不是限制因素，所以通过将tRNA减少到每个所需基因仅一个拷贝，可使总体翻译成本最小化。翻译选择还导致对当前tRNA翻译速度最快的密码子产生偏好；因此，密码子使用和tRNA基因含量将共同进化到一种相互适应的状态。我们表明通常存在不止一种稳定的共同进化状态。这就解释了为什么在同一生物体中不同氨基酸会存在不同的tRNA组合和密码子偏好。我们分析了一组80个完整的细菌基因组，并表明该理论预测了这些数据中出现的许多趋势。
