Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes.
Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes.
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DOI：
10.1371/journal.pgen.1006810
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发表时间：
2017-06
期刊：
影响因子：
4.5
通讯作者：
Forterre P
中科院分区：
文献类型：
--
作者：
Da Cunha V;Gaia M;Gadelle D;Nasir A;Forterre P
真核生物从古细菌中出现的母细胞假说，被元基因组数据中一个新的候选古细菌门“Lokiarchaeota”的描述所支持。根据36个通用蛋白的连接重建的树中Lokiarchaeota的真核分支。然而，个体系统发育揭示了lokiarchaeal蛋白序列具有不同的进化历史。单个标记系统发育揭示了至少两个蛋白质亚群，要么支持Woese生命树，要么支持Eocyte生命树。引人注目的是，去除单个蛋白质，即延伸因子EF2，足以破坏真核生物- lokiarchaea的关系。我们的分析表明，这三种lokiarchaeal EF2蛋白具有嵌合组织，可能是由于污染和/或与真核生物序列斑块的同源重组。一项基于新数据集的RNA聚合酶系统发育分析表明，Lokiarchaeota和Asgard超门的相关门是Euryarchaeota的姐妹类群，而不是真核生物，并支持古细菌的单系性，因为它们的根在分支上导致Thaumarchaeota。人们提出了两种设想来描述我们星球上细胞生命的历史。对于一些作者来说，从最后一个普遍的细胞祖先中出现了两个谱系，一个导致细菌，另一个导致古细菌和真核生物的共同祖先（Woese假说），而另一些人则认为真核生物是从古细菌亚群中出现的（eocyte假说）。后一种假设得到了从环境DNA中重建新的古细菌基因组的支持。这些分析表明真核生物起源于复杂的古细菌，称为Lokiarchaeota，这是最近提出的Asgard超门的第一个描述成员。考虑到这个问题的重要性，我们对来自Lokiarchaea的通用蛋白进行了新的分析，并意识到它们与真核生物的关系很可能是由于不同的偏见，包括嵌合序列和不平等的蛋白质进化速度。从我们的研究结果来看，我们认为Lokiarchaea及其近亲是Euryarchaeota的姊妹类群，而不是真核生物。值得注意的是，我们还表明，在分析中包含的通用标记的选择将严重影响所支持的情景，并且一些标记作为RNA聚合酶支持传统的Woese树。
The eocyte hypothesis, in which Eukarya emerged from within Archaea, has been boosted by the description of a new candidate archaeal phylum, “Lokiarchaeota”, from metagenomic data. Eukarya branch within Lokiarchaeota in a tree reconstructed from the concatenation of 36 universal proteins. However, individual phylogenies revealed that lokiarchaeal proteins sequences have different evolutionary histories. The individual markers phylogenies revealed at least two subsets of proteins, either supporting the Woese or the Eocyte tree of life. Strikingly, removal of a single protein, the elongation factor EF2, is sufficient to break the Eukaryotes-Lokiarchaea affiliation. Our analysis suggests that the three lokiarchaeal EF2 proteins have a chimeric organization that could be due to contamination and/or homologous recombination with patches of eukaryotic sequences. A robust phylogenetic analysis of RNA polymerases with a new dataset indicates that Lokiarchaeota and related phyla of the Asgard superphylum are sister group to Euryarchaeota, not to Eukarya, and supports the monophyly of Archaea with their rooting in the branch leading to Thaumarchaeota. Two scenarios have been proposed to describe the history of cellular life on our planet. For some authors, two lineages emerged from the last universal cellular ancestor, one leading to Bacteria, the other one leading to a common ancestor of Archaea and Eukarya (Woese’s hypothesis), while others suggest that Eukaryotes emerged from within an archaeal subgroup (eocyte hypothesis). This latter hypothesis has been boosted by the reconstruction of new archaeal genomes from environmental DNA. These analyses have suggested that eukaryotes originated from complex archaea, called Lokiarchaeota, the first described members of the recently proposed Asgard superphylum. Considering the importance of this question, we performed new analyses of the universal proteins from Lokiarchaea and realized that their affiliation to Eukaryotes was most probably due to different biases, including chimeric sequences and unequal rate of protein evolution. From our results, we suggest here that Lokiarchaea and close relatives are sister group to Euryarchaeota, not to Eukarya. Notably, we also show that the choices of the universal markers to include in one’s analysis will critically impact the scenario supported and that some markers as the RNA polymerase support the traditional Woese’s tree.