Marine Science Institute, University of California, Santa Barbara, California 93106, USA.
Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA.
Nat Microbiol. 2017 Apr 3;2:17045. doi: 10.1038/nmicrobiol.2017.45.
Major radiations of enigmatic Bacteria and Archaea with large inventories of uncharacterized proteins are a striking feature of the Tree of Life. The processes that led to functional diversity in these lineages, which may contribute to a host-dependent lifestyle, are poorly understood. Here, we show that diversity-generating retroelements (DGRs), which guide site-specific protein hypervariability, are prominent features of genomically reduced organisms from the bacterial candidate phyla radiation (CPR) and as yet uncultivated phyla belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaea) archaeal superphylum. From reconstructed genomes we have defined monophyletic bacterial and archaeal DGR lineages that expand the known DGR range by 120% and reveal a history of horizontal retroelement transfer. Retroelement-guided diversification is further shown to be active in current CPR and DPANN populations, with an assortment of protein targets potentially involved in attachment, defence and regulation. Based on observations of DGR abundance, function and evolutionary history, we find that targeted protein diversification is a pronounced trait of CPR and DPANN phyla compared to other bacterial and archaeal phyla. This diversification mechanism may provide CPR and DPANN organisms with a versatile tool that could be used for adaptation to a dynamic, host-dependent existence.
具有大量特征未知蛋白质的神秘细菌和古菌的主要辐射是生命之树的一个显著特征。导致这些谱系功能多样性的过程，这些谱系可能有助于依赖宿主的生活方式，但人们对此知之甚少。在这里，我们表明，指导特定蛋白质高度可变性的多样性产生 retroelements（DGRs）是细菌候选门辐射（CPR）中基因组减少的生物体以及尚未培养的属于 DPANN（Diapherotrites、Parvarchaeota、Aenigmarchaeota、 Nanoarchaeota 和 Nanohaloarchaea）古菌超门的未培养门的突出特征。从重建的基因组中，我们定义了单系细菌和古菌 DGR 谱系，将已知的 DGR 范围扩大了 120%，并揭示了水平 retroelement 转移的历史。 Retroelement 指导的多样化在当前的 CPR 和 DPANN 种群中进一步显示是活跃的，具有一系列可能涉及附着、防御和调节的潜在蛋白质靶标。基于对 DGR 丰度、功能和进化历史的观察，我们发现与其他细菌和古菌门相比，靶向蛋白质多样化是 CPR 和 DPANN 门的一个显著特征。这种多样化机制可能为 CPR 和 DPANN 生物体提供了一种多功能工具，可用于适应动态的、依赖宿主的生存环境。
