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Arguments Reinforcing the Three-Domain View of Diversified Cellular Life.
Archaea ( IF 2.3 ) Pub Date : 2016-12-05 , DOI: 10.1155/2016/1851865
Arshan Nasir 1 , Kyung Mo Kim 2 , Violette Da Cunha 3 , Gustavo Caetano-Anollés 4
Affiliation  

The archaeal ancestor scenario (AAS) for the origin of eukaryotes implies the emergence of a new kind of organism from the fusion of ancestral archaeal and bacterial cells. Equipped with this “chimeric” molecular arsenal, the resulting cell would gradually accumulate unique genes and develop the complex molecular machineries and cellular compartments that are hallmarks of modern eukaryotes. In this regard, proteins related to phagocytosis and cell movement should be present in the archaeal ancestor, thus identifying the recently described candidate archaeal phylum “Lokiarchaeota” as resembling a possible candidate ancestor of eukaryotes. Despite its appeal, AAS seems incompatible with the genomic, molecular, and biochemical differences that exist between Archaea and Eukarya. In particular, the distribution of conserved protein domain structures in the proteomes of cellular organisms and viruses appears hard to reconcile with the AAS. In addition, concerns related to taxon and character sampling, presupposing bacterial outgroups in phylogenies, and nonuniform effects of protein domain structure rearrangement and gain/loss in concatenated alignments of protein sequences cast further doubt on AAS-supporting phylogenies. Here, we evaluate AAS against the traditional “three-domain” world of cellular organisms and propose that the discovery of Lokiarchaeota could be better reconciled under the latter view, especially in light of several additional biological and technical considerations.

中文翻译:

支持多样化细胞生命三领域观点的论点。

真核生物起源的古细菌祖先情景(AAS)意味着一种新的生物从祖先古细菌和细菌细胞的融合中出现。配备这种“嵌合”分子武器库,由此产生的细胞将逐渐积累独特的基因,并发展出现代真核生物标志性的复杂分子机制和细胞区室。在这方面,与吞噬作用和细胞运动相关的蛋白质应该存在于古细菌祖先中,从而确定最近描述的候选古细菌门“Lokiarchaeota”类似于真核生物的可能候选祖先。尽管具有吸引力,但 AAS 似乎与古生菌和真核生物之间存在的基因组、分子和生化差异不相容。特别是,细胞生物和病毒蛋白质组中保守蛋白质结构域结构的分布似乎很难与 AAS 协调一致。此外,与分类单元和特征采样、假设系统发育中的细菌外群以及蛋白质结构域结构重排和蛋白质序列串联比对中的增益/损失的不均匀影响有关的担忧进一步质疑了支持 AAS 的系统发育。在这里,我们针对传统的“三域”细胞生物世界评估 AAS,并建议在后一种观点下发现 Lokiarchaeota 可以更好地协调一致,特别是考虑到一些额外的生物学和技术考虑。假设系统发育中的细菌外群,以及蛋白质结构域重排和蛋白质序列连接比对中的增益/丢失的不均匀影响,进一步质疑支持 AAS 的系统发育。在这里,我们针对传统的“三域”细胞生物世界评估 AAS,并建议在后一种观点下发现 Lokiarchaeota 可以更好地协调一致,特别是考虑到一些额外的生物学和技术考虑。假设系统发育中的细菌外群,以及蛋白质结构域重排和蛋白质序列连接比对中的增益/丢失的不均匀影响,进一步质疑支持 AAS 的系统发育。在这里,我们针对传统的“三域”细胞生物世界评估 AAS,并建议在后一种观点下发现 Lokiarchaeota 可以更好地协调一致,特别是考虑到一些额外的生物学和技术考虑。
更新日期:2016-12-05
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