Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris 75015, France.
Nucleic Acids Res. 2021 Mar 18;49(5):2655-2673. doi: 10.1093/nar/gkab064.
Plasmids and temperate phages are key contributors to bacterial evolution. They are usually regarded as very distinct. However, some elements, termed phage-plasmids, are known to be both plasmids and phages, e.g. P1, N15 or SSU5. The number, distribution, relatedness and characteristics of these phage-plasmids are poorly known. Here, we screened for these elements among ca. 2500 phages and 12000 plasmids and identified 780 phage-plasmids across very diverse bacterial phyla. We grouped 92% of them by similarity of gene repertoires to eight defined groups and 18 other broader communities of elements. The existence of these large groups suggests that phage-plasmids are ancient. Their gene repertoires are large, the average element is larger than an average phage or plasmid, and they include slightly more homologs to phages than to plasmids. We analyzed the pangenomes and the genetic organization of each group of phage-plasmids and found the key phage genes to be conserved and co-localized within distinct groups, whereas genes with homologs in plasmids are much more variable and include most accessory genes. Phage-plasmids are a sizeable fraction of the sequenced plasmids (∼7%) and phages (∼5%), and could have key roles in bridging the genetic divide between phages and other mobile genetic elements.
质粒和温和噬菌体是细菌进化的主要贡献者。它们通常被认为是非常不同的。然而，一些被称为噬菌体-质粒的元素，既可以是质粒，也可以是噬菌体，例如 P1、N15 或 SSU5。这些噬菌体-质粒的数量、分布、相关性和特征知之甚少。在这里，我们在大约 2500 个噬菌体和 12000 个质粒中筛选这些元素，在非常不同的细菌门中鉴定了 780 个噬菌体-质粒。我们根据基因库的相似性将它们分为 8 个定义的组和 18 个其他更广泛的元素群落，其中 92%的组与定义的组相似。这些大型群组的存在表明噬菌体-质粒是古老的。它们的基因库很大，平均元素比平均噬菌体或质粒大，并且它们包含的噬菌体同源物略多于质粒。我们分析了噬菌体-质粒的每个群组的泛基因组和遗传组织，并发现关键的噬菌体基因在不同的群组中保守且共定位，而与质粒具有同源物的基因则变化更大，并且包含大多数辅助基因。噬菌体-质粒是已测序质粒（约 7%）和噬菌体（约 5%）的重要组成部分，可能在弥合噬菌体和其他移动遗传元件之间的遗传鸿沟方面发挥关键作用。
