Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox.
Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox.
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DOI：
10.1186/gb-2004-5-3-r17
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发表时间：
2004
期刊：
影响因子：
12.3
通讯作者：
Gribaldo S
中科院分区：
文献类型：
--
作者：
Brochier C;Forterre P;Gribaldo S
本文基于转录和翻译蛋白组对古细菌进行了系统发育分析。系统发育揭示了 Methanopyrus kandleri 的进化地位。古细菌的系统发育分析主要通过16S rRNA序列比较来建立。随着完全测序的基因组的积累，现在可以通过使用大型序列数据集来测试替代方法。我们使用两个串联数据集分析了古菌系统发育，该数据集由 14 个参与转录的蛋白质和 53 个核糖体蛋白质（分别为 3,275 和 6,377 个位置）组成。重要的关系得到了证实，特别是古菌领域的二分法，以 Crenarchaeota 和 Euryarchaeota 为代表，Sulfolobales 和 Aeropyrum pernix 的姐妹群，以及由热原体目、Archaeoglobus fulgidus、Methanosarcinales 和 Halobacteriales 组成的大类群的单系性，后两个目形成了一个强大的群体 簇。主要区别在于 Methanopyrus kandleri 的位置，它在翻译树中与甲烷球菌目和甲烷杆菌目分组，而它在转录树中出现在广古菌的底部。 M. kandleri 的不一致位置很可能是重建伪影的结果，因为其转录装置的组件显示出高进化率。我们证明转录和翻译这两个信息系统为古菌系统发育提供了基本一致的信号。特别是，我们的分析支持热球菌分支后出现产甲烷作用，以及产甲烷祖先内部较晚出现有氧呼吸。我们讨论了 M. kandleri 转录机制的进化加速与该古菌的几个独特特征之间可能的联系，特别是延伸转录因子 TFS 的缺失。
This article presents a phylogenetic analysis of the Archea based on sets of transcription and translation proteins. The phylogenies shed light on the evolutionary position of Methanopyrus kandleri. Phylogenetic analysis of the Archaea has been mainly established by 16S rRNA sequence comparison. With the accumulation of completely sequenced genomes, it is now possible to test alternative approaches by using large sequence datasets. We analyzed archaeal phylogeny using two concatenated datasets consisting of 14 proteins involved in transcription and 53 ribosomal proteins (3,275 and 6,377 positions, respectively). Important relationships were confirmed, notably the dichotomy of the archaeal domain as represented by the Crenarchaeota and Euryarchaeota, the sister grouping of Sulfolobales and Aeropyrum pernix, and the monophyly of a large group comprising Thermoplasmatales, Archaeoglobus fulgidus, Methanosarcinales and Halobacteriales, with the latter two orders forming a robust cluster. The main difference concerned the position of Methanopyrus kandleri, which grouped with Methanococcales and Methanobacteriales in the translation tree, whereas it emerged at the base of the euryarchaeotes in the transcription tree. The incongruent placement of M. kandleri is likely to be the result of a reconstruction artifact due to the high evolutionary rates displayed by the components of its transcription apparatus. We show that two informational systems, transcription and translation, provide a largely congruent signal for archaeal phylogeny. In particular, our analyses support the appearance of methanogenesis after the divergence of the Thermococcales and a late emergence of aerobic respiration from within methanogenic ancestors. We discuss the possible link between the evolutionary acceleration of the transcription machinery in M. kandleri and several unique features of this archaeon, in particular the absence of the elongation transcription factor TFS.
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DOI：
10.1073/pnas.1030608100
发表时间：
2003-06-10
影响因子：
11.1
作者：
Armache, KJ;Kettenberger, H;Cramer, P
通讯作者：
Cramer, P
影响因子：
6.5
作者：
DeLong, EE;Pace, NR
通讯作者：
Pace, NR
影响因子：
4.8
作者：
Awrey, DE;Weilbaecher, RG;Edwards, AM
通讯作者：
Edwards, AM
影响因子：
56.9
作者：
ERIE, DA;HAJISEYEDJAVADI, O;VONHIPPEL, PH
通讯作者：
VONHIPPEL, PH
影响因子：
6.5
作者：
Felsenstein, J
通讯作者：
Felsenstein, J