Tirumalai Madhan R, Sivaraman Raghavan V, Kutty Layla A, Song Eric L, Fox George E
Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA.
Silver Lab, Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA.
Archaea. 2023 Sep 29;2023:5512414. doi: 10.1155/2023/5512414. eCollection 2023.
It has been proposed that the superphylum of Asgard Archaea may represent a historical link between the Archaea and Eukarya. Following the discovery of the Archaea, it was soon appreciated that archaeal ribosomes were more similar to those of Eukarya rather than Bacteria. Coupled with other eukaryotic-like features, it has been suggested that the Asgard Archaea may be directly linked to eukaryotes. However, the genomes of Bacteria and non-Asgard Archaea generally organize ribosome-related genes into clusters that likely function as operons. In contrast, eukaryotes typically do not employ an operon strategy. To gain further insight into conservation of the r-protein genes, the genome order of conserved ribosomal protein (r-protein) coding genes was identified in 17 Asgard genomes (thirteen complete genomes and four genomes with less than 20 contigs) and compared with those found previously in non-Asgard archaeal and bacterial genomes. A universal core of two clusters of 14 and 4 cooccurring r-proteins, respectively, was identified in both the Asgard and non-Asgard Archaea. The equivalent genes in the version of the cluster are found in the and operons. The large cluster of 14 r-protein genes ( from the operon and from the operon) occurs as a complete set in the genomes of thirteen Asgard genomes (five Lokiarchaeotes, three Heimdallarchaeotes, one Odinarchaeote, and four Thorarchaeotes). Four less conserved clusters with partial bacterial equivalents were found in the Asgard. These were the ( operon in Bacteria) cluster, the ( operon in Bacteria) cluster, the cluster, and the , cluster. Finally, a new cluster referred to as was identified. In many cases, r-protein gene clusters/operons are less conserved in their organization in the Asgard group than in other Archaea. If this is generally true for nonribosomal gene clusters, the results may have implications for the history of genome organization. In particular, there may have been an early transition to or from the operon approach to genome organization. Other nonribosomal cellular features may support different relationships. For this reason, it may be important to consider ribosome features separately.
有人提出，阿斯加德古菌超群可能代表了古菌和真核生物之间的历史联系。在发现古菌之后，人们很快认识到古菌核糖体与真核生物的核糖体比与细菌的核糖体更相似。再加上其他类似真核生物的特征，有人认为阿斯加德古菌可能与真核生物直接相关。然而，细菌和非阿斯加德古菌的基因组通常将核糖体相关基因组织成可能作为操纵子发挥作用的簇。相比之下，真核生物通常不采用操纵子策略。为了进一步深入了解核糖体蛋白基因的保守性，在17个阿斯加德基因组（13个完整基因组和4个重叠群少于20个的基因组）中确定了保守核糖体蛋白（r蛋白）编码基因的基因组顺序，并与之前在非阿斯加德古菌和细菌基因组中发现的顺序进行了比较。在阿斯加德古菌和非阿斯加德古菌中分别鉴定出了两个分别由14个和4个共同出现的r蛋白组成的普遍核心簇。该簇版本中的等效基因存在于和操纵子中。14个r蛋白基因的大簇（来自操纵子的和来自操纵子的）在13个阿斯加德基因组（5个洛基古菌、3个海姆达尔古菌、1个奥丁古菌和4个索尔古菌）的基因组中作为一个完整的集合出现。在阿斯加德中发现了4个保守性较低的簇，它们与部分细菌等效。这些是（细菌中的操纵子）簇、（细菌中的操纵子）簇、簇和、簇。最后，鉴定出了一个新的簇，称为。在许多情况下，阿斯加德组中r蛋白基因簇/操纵子的组织保守性低于其他古菌。如果对于非核糖体基因簇普遍如此，那么这些结果可能对基因组组织的历史有影响。特别是，可能存在从操纵子方法到基因组组织的早期转变或从基因组组织到操纵子方法的早期转变。其他非核糖体细胞特征可能支持不同的关系。因此，单独考虑核糖体特征可能很重要。
