Caetano-Anolles Gustavo, Sun Feng-Jie, Wang Minglei, Yafremava Liudmila S, Harish Ajith, Kim Hee Shin, Knudsen Vegeir, Caetano-Anolles Derek, Mittenthal Jay E
Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA.
Front Biosci. 2008 May 1;13:5212-40. doi: 10.2741/3077.
The survey of components in living systems at different levels of organization enables an evolutionary exploration of patterns and processes in macromolecules, networks, and genomic repertoires. Here we discuss how phylogenetic strategies that generate intrinsically rooted phylogenies impact the evolutionary study of RNA and protein components of the macromolecular machinery that is responsible for biological function. We used these methods to generate timelines of discovery of components in systems, such as substructures in RNA molecules, architectures in proteomes, domains in multi-domain proteins, enzymes in metabolic networks, and protein architectures in proteomes. These timelines unfolded remarkable patterns of origin and evolution of molecules, repertoires and networks, showing episodes of both functional specialization (e.g., rise of domains with specialized functions) and molecular simplification (e.g., reductive tendencies in molecules and proteomes). These observations have important evolutionary implications for origins of translation, the genetic code, modules in the protein world, and diversification of life, and suggest early evolution of modern biochemistry was driven by recruitment of both RNA and protein catalysts in an ancient community of complex organisms.
对不同组织层次的生命系统中的成分进行调查，有助于对大分子、网络和基因组库中的模式和过程进行进化探索。在这里，我们讨论了生成内在有根系统发育树的系统发育策略如何影响负责生物功能的大分子机制的RNA和蛋白质成分的进化研究。我们使用这些方法来生成系统中成分发现的时间线，例如RNA分子中的亚结构、蛋白质组中的结构、多结构域蛋白质中的结构域、代谢网络中的酶以及蛋白质组中的蛋白质结构。这些时间线展现出分子、库和网络起源与进化的显著模式，显示出功能特化（例如，具有特定功能的结构域的出现）和分子简化（例如，分子和蛋白质组中的还原趋势）的阶段。这些观察结果对翻译的起源、遗传密码、蛋白质世界中的模块以及生命的多样化具有重要的进化意义，并表明现代生物化学的早期进化是由古代复杂生物群落中RNA和蛋白质催化剂的招募驱动的。
