A korarchaeal genome reveals insights into the evolution of the Archaea
A korarchaeal genome reveals insights into the evolution of the Archaea
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DOI：
10.1073/pnas.0801980105
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发表时间：
2008-06-10
影响因子：
11.1
通讯作者：
Stetter, Karl O.
中科院分区：
文献类型：
--
作者：
Elkins, James G.;Podar, Mircea;Stetter, Karl O.
候选科尔考古门由一组未培养的微生物组成，根据它们的小亚单位rRNA系统发育，这些微生物可能很早就与主要的古生物门克伦考古塔和Eurya chaeota分化开来。在这里，我们报告了一个科尔考古群成员的初步特征，建议将其命名为“Candidatus Kor考古um Cryptofilum”，它显示出超薄的丝状形态。为了研究深分枝的考古科与其他门之间可能的祖先关系，我们使用全基因组鸟枪测序从丰富的细胞中构建了一个完整的复合科尔古科基因组。基因组被组装成一个1.59Mb的单一重叠群，G+C含量为49%。在1,617个预测的蛋白质编码基因中，1,382个(85%)可能被归入一组修订的古生代同源类群(CoG)。预测的基因功能表明，该生物体依赖于一种简单的多肽发酵模式来获得碳和能量，并且缺乏合成从头开始的嘌呤、辅酶A和其他几种辅因子的能力。基于保守的单基因和串联蛋白序列的系统发育分析将科尔考古特定位为一个深层次的古生物谱系，与克伦考古群有明显的亲缘关系。然而，预测的基因含量显示，一些保守的细胞系统，如细胞分裂、DNA复制和tRNA成熟，与Eurya chaeota中的对应系统相似。根据已知的古生物基因组的组成，科考古塔人可能保留了一组代表祖先古生物形式的细胞特征。
The candidate division Korarchaeota comprises a group of uncultivated microorganisms that, by their small subunit rRNA phylogeny, may have diverged early from the major archaeal phyla Crenarchaeota and Euryarchaeota. Here, we report the initial characterization of a member of the Korarchaeota with the proposed name, "Candidatus Korarchaeum cryptofilum," which exhibits an ultrathin filamentous morphology. To investigate possible ancestral relationships between deep-branching Korarchaeota and other phyla, we used whole-genome shotgun sequencing to construct a complete composite korarchaeal genome from enriched cells. The genome was assembled into a single contig 1.59 Mb in length with a G + C content of 49%. Of the 1,617 predicted protein-coding genes, 1,382,(85%) could be assigned to a revised set of archaeal Clusters of Orthologous Groups (COGs). The predicted gene functions suggest that the organism relies on a simple mode of peptide fermentation for carbon and energy and lacks the ability to synthesize de novo purines, CoA, and several other cofactors. Phylogenetic analyses based on conserved single genes and concatenated protein sequences positioned the korarchaeote as a deep archaeal lineage with an apparent affinity to the Crenarchaeota. However, the predicted gene content revealed that several conserved cellular systems, such as cell division, DNA replication, and tRNA maturation, resemble the counterparts in the Euryarchaeota. In light of the known composition of archaeal genomes, the Korarchaeota might have retained a set of cellular features that represents the ancestral archaeal form.