Analysis of phenetic trees based on metabolic capabilites across the three domains of life
Analysis of phenetic trees based on metabolic capabilites across the three domains of life
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DOI：
10.1016/j.jmb.2004.04.059
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发表时间：
2004-07-09
影响因子：
5.6
通讯作者：
Sternberg, MJE
中科院分区：
文献类型：
--
作者：
Aguilar, D;Aviles, FX;Sternberg, MJE
在这里，我们使用完整的基因组数据来比较研究不同物种的代谢。我们根据新陈代谢的不同部分中存在的酶功能构建了基因树。比较分析了真核生物、细菌和古生界的27种生物的7大代谢类，包括总共69条代谢途径。根据每个代谢类别的酶功能的存在/不存在来确定系统发育谱，然后从谱中得出所有生物体的距离矩阵。基于矩阵的无根遗传树揭示了生物根据其代谢能力的分布，反映了这些物种在进化过程中所经历的生态压力和适应。我们发现，在系统发育方面密切相关的生物在新陈代谢方面可能存在遥远的亲缘关系，反之亦然。例如，专性细菌病原体通常在我们的代谢树中聚在一起，这表明专性病原体具有共同的代谢特征，无论它们的系统发育来源是什么。蛋白细菌的分支顺序往往与其经典的系统发育分类不符，革兰氏阳性菌表现出不同的代谢亲和力。古生菌被发现在代谢上与自由生活的细菌的距离与真核生物的距离一样远，有时被放置在代谢高度专门化的专性细菌病原体群附近。代谢树代表了一种综合方法，用于比较新陈代谢的进化及其与基因组进化的相关性，有助于在生命树中找到新的关系。(C)2004爱思唯尔有限公司。保留所有权利。
Here, we used data of complete genomes to study comparatively the metabolism of different species. We built phenetic trees based on the enzymatic functions present in different parts of metabolism. Seven broad metabolic classes, comprising a total of 69 metabolic pathways, were comparatively analyzed for 27 fully sequenced organisms of the domains Eukarya, Bacteria and Archaea. Phylogenetic profiles based on the presence/absence of enzymatic functions for each metabolic class were determined and distance matrices for all the organisms were then derived from the profiles. Unrooted phenetic trees based upon the matrices revealed the distribution of the organisms according to their metabolic capabilities, reflecting the ecological pressures and adaptations that those species underwent during their evolution. We found that organisms that are closely related in phylogenetic terms could be distantly related metabolically and that the opposite is also true. For example, obligate bacterial pathogens were usually grouped together in our metabolic trees, demonstrating that obligate pathogens share common metabolic features regardless of their diverse phylogenetic origins. The branching order of proteobacteria often did not match their classical phylogenetic classification and Gram-positive bacteria showed diverse metabolic affinities. Archaea were found to be metabolically as distant from free-living bacteria as from eukaryotes, and sometimes were placed close to the metabolically highly specialized group of obligate bacterial pathogens. Metabolic trees represent an integrative approach for the comparison of the evolution of the metabolism and its correlation with the evolution of the genome, helping to find new relationships in the tree of life. (C) 2004 Elsevier Ltd. All rights reserved.