Rabbani Mahnaz, Wahl Lindi M
Applied Mathematics, Western University, London, Ontario, Canada N6A 5B7.
Applied Mathematics, Western University, London, Ontario, Canada N6A 5B7.
J Theor Biol. 2016 Oct 21;407:401-408. doi: 10.1016/j.jtbi.2016.07.030. Epub 2016 Jul 25.
Mobile promoters are emerging as a new class of mobile genetic elements, first identified by examining prokaryote genome sequences, and more recently confirmed by experimental observations in bacteria. Recent datasets have identified over 40,000 putative mobile promoters in sequenced prokaryote genomes, however only one-third of these are in regions of the genome directly upstream from coding sequences, that is, in promoter regions. The presence of many promoter sequences in non-promoter regions is unexplained. Here we develop a general mathematical model for the dynamics of mobile promoters, extending previous work to capture the dynamics both within and outside promoter regions. From this general model, we apply rigorous model selection techniques to identify which parameters are statistically justified in describing the available mobile promoter data, and find best-fit values of these parameters. Our results suggest that high rates of horizontal gene transfer maintain the population of mobile promoters in promoter regions, and that once established at these sites, mobile promoters are rarely lost, but are commonly copied to other genomic regions. In contrast, mobile promoter copies in non-promoter regions are more numerous and more volatile, experiencing substantially higher rates of duplication, loss and diversification.
移动启动子正作为一类新型的可移动遗传元件出现，最初是通过检查原核生物基因组序列而被发现的，最近在细菌中的实验观察也证实了这一点。最近的数据集在已测序的原核生物基因组中鉴定出了超过40000个假定的移动启动子，然而其中只有三分之一位于基因组中编码序列直接上游的区域，即启动子区域。非启动子区域中存在许多启动子序列的原因尚不清楚。在这里，我们为移动启动子的动力学建立了一个通用的数学模型，扩展了先前的工作以捕捉启动子区域内外的动力学。从这个通用模型出发，我们应用严格的模型选择技术来确定哪些参数在描述现有的移动启动子数据时在统计上是合理的，并找到这些参数的最佳拟合值。我们的结果表明，高水平的水平基因转移维持了启动子区域中移动启动子的数量，并且一旦在这些位点建立，移动启动子很少丢失，但通常会被复制到其他基因组区域。相比之下，非启动子区域中的移动启动子拷贝数量更多且更不稳定，经历的复制、丢失和多样化速率要高得多。
