Department of Molecular and Cell Biology, University of Connecticut, CT, USA.
Mol Biol Evol. 2010 Aug;27(8):1792-801. doi: 10.1093/molbev/msq057. Epub 2010 Mar 1.
The origin of the genetic code and the rooting of the tree of life (ToL) are two of the most challenging problems in the study of life's early evolution. Although both have been the focus of numerous investigations utilizing a variety of methods, until now, each problem has been addressed independently. Typically, attempts to root the ToL have relied on phylogenies of genes with ancient duplications, which are subject to artifacts of tree reconstruction and horizontal gene transfer, or specific physiological characters believed to be primitive, which are often based on subjective criteria. Here, we demonstrate a unique method for rooting based on the identification of amino acid usage biases comprising the residual signature of a more primitive genetic code. Using a phylogenetic tree of concatenated ribosomal proteins, our analysis of amino acid compositional bias detects a strong and unique signal associated with the early expansion of the genetic code, placing the root of the translation machinery along the bacterial branch.
遗传密码的起源和生命之树（ToL）的根源是生命早期进化研究中最具挑战性的两个问题。尽管这两个问题都一直是利用各种方法进行了大量研究的焦点，但到目前为止，每个问题都是独立解决的。通常，对 ToL 进行扎根的尝试依赖于具有古老复制的基因的系统发育，这些基因受到树重建和水平基因转移的伪影的影响，或者依赖于被认为是原始的特定生理特征，而这些特征通常基于主观标准。在这里，我们展示了一种基于识别氨基酸使用偏倚的独特方法，该方法由更原始的遗传密码的残余特征组成。使用核糖体蛋白的串联系统发育树，我们对氨基酸组成偏倚的分析检测到与遗传密码早期扩展相关的强烈而独特的信号，从而将翻译机制的根置于细菌分支上。
