The Candidate Phyla Radiation (CPR) is a proposed subdivision within the bacterial domain comprising of several candidate phyla. CPR microorganisms are united by small genome and physical sizes, lack several metabolic enzymes, and populate deep branches within the bacterial subtree of life. These features raise intriguing questions regarding their origin and mode of evolution. In this study, we performed a comparative and phylogenomic analysis to investigate CPR origin and evolution. Unlike previous gene/protein sequence-based reports of CPR evolution, we used protein domain superfamilies classified by protein structure databases to resolve the evolutionary relationships of CPR with non-CPR bacteria, Archaea, Eukarya, and viruses. Across all supergroups, CPR shared maximum superfamilies with non-CPR bacteria and were placed as deep branching bacteria in most phylogenomic trees. CPR contributed 1.22% new superfamilies to bacteria including the ribosomal protein L19e and encoded 4 core superfamilies that are likely involved in cell-to-cell interaction and establishing epi-symbiotic lifestyles. While CPR and non-CPR bacterial proteomes gained common superfamilies over the course of evolution, CPR and Archaea had more common losses. These losses mostly involved metabolic superfamilies. In fact, phylogenies built from only metabolic protein superfamilies separated CPR and non-CPR bacteria. These findings indicate that CPR are bacterial microorganisms that have probably evolved in an Archaea-like manner via the early loss of key metabolic functions. We also discovered that phylogenies built from metabolic and informational superfamilies gave contrasting views of the groupings among Archaea, Bacteria, and Eukarya, which add to the current debate on the evolutionary relationships among superkingdoms.

中文翻译：

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CPR 群的细菌起源和还原进化。


候选门辐射（CPR）是细菌域内的一个拟议细分，由几个候选门组成。 CPR微生物通过较小的基因组和物理尺寸结合在一起，缺乏多种代谢酶，并在细菌生命子树中占据较深的分支。这些特征引发了关于它们的起源和进化模式的有趣问题。在这项研究中，我们进行了比较和系统发育分析，以研究 CPR 的起源和进化。与之前基于基因/蛋白质序列的CPR进化报告不同，我们使用蛋白质结构数据库分类的蛋白质结构域超家族来解析CPR与非CPR细菌、古细菌、真核生物和病毒的进化关系。在所有超群中，CPR 与非 CPR 细菌共享最大的超科，并且在大多数系统发育树中被放置为深分支细菌。 CPR 为细菌贡献了 1.22% 的新超家族，包括核糖体蛋白 L19e，并编码了 4 个可能参与细胞间相互作用和建立表共生生活方式的核心超家族。虽然 CPR 和非 CPR 细菌蛋白质组在进化过程中获得了共同的超家族，但 CPR 和古细菌的损失更为常见。这些损失主要涉及代谢超家族。事实上，仅由代谢蛋白超家族构建的系统发育将 CPR 和非 CPR 细菌分开。这些发现表明，CPR 是细菌微生物，可能通过关键代谢功能的早期丧失以类似古细菌的方式进化。 我们还发现，从代谢和信息超科构建的系统发育对古细菌、细菌和真核生物之间的分类给出了截然不同的观点，这加剧了当前关于超界之间进化关系的争论。