Rooting the Ribosomal Tree of Life
Rooting the Ribosomal Tree of Life
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DOI：
10.1093/molbev/msq057
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发表时间：
2010-08-01
影响因子：
10.7
通讯作者：
Gogarten, J. Peter
中科院分区：
文献类型：
--
作者：
Fournier, Gregory P.;Gogarten, J. Peter
遗传密码的起源和生命之树的起源是生命早期进化研究中最具挑战性的两个问题。尽管这两个问题都是利用各种方法进行大量研究的焦点，但到目前为止，每个问题都是独立解决的。通常，对ToL进行根底的尝试依赖于具有古代复制的基因的系统发育，这受到树重建和水平基因转移的影响，或者被认为是原始的特定生理特征，这通常基于主观标准。在这里，我们展示了一种独特的生根方法，该方法基于氨基酸使用偏差的识别，包括更原始的遗传密码的残余特征。利用连接核糖体蛋白的系统发育树，我们对氨基酸组成偏差的分析发现了一个与遗传密码早期扩展相关的强烈而独特的信号，将翻译机制的根沿着细菌分支放置。
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.