Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, United States of America.
PLoS One. 2021 Mar 26;16(3):e0247806. doi: 10.1371/journal.pone.0247806. eCollection 2021.
Upon discovery of the first archaeal species in the 1970s, life has been subdivided into three domains: Eukarya, Archaea, and Bacteria. However, the organization of the three-domain tree of life has been challenged following the discovery of archaeal lineages such as the TACK and Asgard superphyla. The Asgard Superphylum has emerged as the closest archaeal ancestor to eukaryotes, potentially improving our understanding of the evolution of life forms. We characterized the transportomes and their substrates within four metagenome-assembled genomes (MAGs), that is, Odin-, Thor-, Heimdall- and Loki-archaeota as well as the fully sequenced genome of Candidatus Prometheoarchaeum syntrophicum strain MK-D1 that belongs to the Loki phylum. Using the Transporter Classification Database (TCDB) as reference, candidate transporters encoded within the proteomes were identified based on sequence similarity, alignment coverage, compatibility of hydropathy profiles, TMS topologies and shared domains. Identified transport systems were compared within the Asgard superphylum as well as within dissimilar eukaryotic, archaeal and bacterial organisms. From these analyses, we infer that Asgard organisms rely mostly on the transport of substrates driven by the proton motive force (pmf), the proton electrochemical gradient which then can be used for ATP production and to drive the activities of secondary carriers. The results indicate that Asgard archaea depend heavily on the uptake of organic molecules such as lipid precursors, amino acids and their derivatives, and sugars and their derivatives. Overall, the majority of the transporters identified are more similar to prokaryotic transporters than eukaryotic systems although several instances of the reverse were documented. Taken together, the results support the previous suggestions that the Asgard superphylum includes organisms that are largely mixotrophic and anaerobic but more clearly define their metabolic potential while providing evidence regarding their relatedness to eukaryotes.
在 20 世纪 70 年代发现第一种古菌后，生命被细分为三个域：真核生物、古菌和细菌。然而，随着 TACK 和 Asgard 超门等古菌谱系的发现，三界生命树的组织受到了挑战。Asgard 超门已成为与真核生物最接近的古菌祖先，这可能有助于我们更好地理解生命形式的进化。我们对四个宏基因组组装基因组（MAG）中的转运体及其底物进行了表征，即 Odin、Thor、Heimdall 和 Loki 古菌，以及属于 Loki 门的完全测序的 Candidatus Prometheoarchaeum syntrophicum 菌株 MK-D1 的基因组。使用转运蛋白分类数据库（TCDB）作为参考，根据序列相似性、比对覆盖率、疏水性图谱的兼容性、TMS 拓扑结构和共享结构域，在蛋白质组中鉴定候选转运蛋白。在 Asgard 超门内以及在不同的真核生物、古菌和细菌生物体内比较鉴定的转运系统。从这些分析中，我们推断 Asgard 生物主要依赖于质子动力势（pmf）驱动的底物转运，质子电化学梯度可用于 ATP 产生并驱动次级载体的活性。结果表明，Asgard 古菌严重依赖于有机分子如脂质前体、氨基酸及其衍生物以及糖及其衍生物的摄取。总的来说，大多数鉴定出的转运蛋白与原核转运蛋白更相似，而不是真核系统，尽管也有一些相反的情况。总的来说，这些结果支持了之前的观点，即 Asgard 超门包括主要是混养和厌氧的生物，但更明确地定义了它们的代谢潜力，并提供了它们与真核生物相关的证据。
