del Grande Marc, Moreno-Hagelsieb Gabriel
Department of Biology, Wilfrid Laurier University, 75 University Ave, W,, N2L 3C5 Waterloo, Ontario, Canada.
BMC Res Notes. 2014 Dec 17;7:928. doi: 10.1186/1756-0500-7-928.
Tests for the evolutionary conservation of associations between genes coding for transcription factors (TFs) and other genes have been limited to a few model organisms due to the lack of experimental information of functional associations in other organisms. We aimed at surmounting this limitation by using the most co-occurring gene pairs as proxies for the most conserved functional interactions available for each gene in a genome. We then used genes predicted to code for TFs to compare their most conserved interactions against the most conserved interactions for the rest of the genes within each prokaryotic genome available.
We plotted profiles of phylogenetic profiles, p-cubic, to compare the maximally scoring interactions of TFs against those of other genes. In most prokaryotes, genes coding for TFs showed lower co-occurrences when compared to other genes. We also show that genes coding for TFs tend to have lower Codon Adaptation Indexes compared to other genes.
The co-occurrence tests suggest that transcriptional regulation evolves quickly in most, if not all, prokaryotes. The Codon Adaptation Index analyses suggest quick gene exchange and rewiring of transcriptional regulation across prokaryotes.
由于缺乏其他生物中功能关联的实验信息，对编码转录因子（TFs）的基因与其他基因之间关联的进化保守性测试仅限于少数模式生物。我们旨在通过使用共现频率最高的基因对作为基因组中每个基因可获得的最保守功能相互作用的代理来克服这一限制。然后，我们使用预测编码TFs的基因，将其最保守的相互作用与每个可用原核生物基因组中其余基因的最保守相互作用进行比较。
我们绘制了系统发育图谱（p-立方），以比较TFs与其他基因的最高得分相互作用。在大多数原核生物中，与其他基因相比，编码TFs的基因共现频率较低。我们还表明，与其他基因相比，编码TFs的基因往往具有较低的密码子适应指数。
共现测试表明，转录调控在大多数（如果不是全部）原核生物中进化迅速。密码子适应指数分析表明，原核生物之间转录调控的基因交换和重新布线迅速。
