Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea.
Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea.
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DOI：
10.1038/nmicrobiol.2017.45
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发表时间：
2017-04-03
影响因子：
28.3
通讯作者：
Valentine DL
中科院分区：
文献类型：
--
作者：
Paul BG;Burstein D;Castelle CJ;Handa S;Arambula D;Czornyj E;Thomas BC;Ghosh P;Miller JF;Banfield JF;Valentine DL
具有大量未知蛋白质的神秘细菌和古细菌的主要辐射是生命之树的一个显著特征。导致这些谱系中功能多样性的过程，可能导致依赖宿主的生活方式，但人们对其了解甚少。在这里，我们发现多样性生成逆转录因子（DGRs）是细菌候选门辐射（CPR）和属于DPANN古细菌超门的未培养门的基因组减少生物的突出特征，它指导位点特异性蛋白质的高变异性。从重建的基因组中，我们定义了单系细菌和古细菌的DGR谱系，将已知的DGR范围扩大了120%，并揭示了水平逆转录因子转移的历史。在当前的CPR和DPANN群体中，retroelement引导的多样化进一步被证明是活跃的，各种各样的蛋白质靶标可能涉及附着、防御和调节。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细菌门相比，CPR和DPANN门的靶向蛋白多样化是一个显著的特征。这种多样化机制可能为CPR和DPANN生物提供了一种多功能工具，可用于适应动态的、依赖宿主的存在。
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 yet uncultivated phyla belonging to the DPANN archaeal superphylum. From reconstructed genomes we defined monophyletic bacterial and archaeal DGR lineages that expand 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, defense, 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 a versatile tool that could be used for adaptation to a dynamic, host-dependent, existence.