Department of Biochemistry, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas Sols-Morreale (CSIC-UAM), Madrid, Spain.
Nucleic Acids Res. 2024 Nov 11;52(20):12498-12516. doi: 10.1093/nar/gkae891.
Defense genes gather in diverse types of genomic islands in bacteria and provide immunity against viruses and other genetic mobile elements. Here, we disclose pipolins, previously found in diverse bacterial phyla and encoding a primer-independent PolB, as a new category of widespread defense islands. The analysis of the occurrence and structure of pipolins revealed that they are commonly integrative elements flanked by direct repeats in Gammaproteobacteria genomes, mainly Escherichia, Vibrio or Aeromonas, often taking up known mobile elements integration hotspots. Remarkably, integrase dynamics correlates with alternative integration spots and enables diverse lifestyles, from integrative to mobilizable and plasmid pipolins, such as in members of the genera Limosilactobacillus, Pseudosulfitobacter or Staphylococcus. Pipolins harbor a minimal core and a large cargo module enriched for defense factors. In addition, analysis of the weighted gene repertoire relatedness revealed that many of these defense factors are actively exchanged with other mobile elements. These findings indicate pipolins and, potentially other defense islands, act as orthogonal reservoirs of defense genes, potentially transferable to immune autonomous MGEs, suggesting complementary exchange mechanisms for defense genes in bacterial populations.
防御基因聚集在细菌的多种基因组岛中，为病毒和其他遗传移动元件提供免疫。在这里，我们揭示了以前在多种细菌门中发现的 pipolins，它编码一种不依赖引物的 PolB，是一种新的广泛防御岛类别。对 pipolins 的发生和结构的分析表明，它们通常是整合元件，在 Gammaproteobacteria 基因组中侧翼是直接重复序列，主要是 Escherichia、Vibrio 或 Aeromonas，它们经常占据已知的移动元件整合热点。值得注意的是，整合酶的动态与替代整合点相关，使它们能够具有多种生活方式，从整合到可移动和质粒 pipolins，例如 Limosilactobacillus、Pseudosulfitobacter 或 Staphylococcus 属的成员。pipolins 具有最小的核心和富含防御因子的大型货物模块。此外，加权基因库相关性分析表明，这些防御因子中的许多都与其他移动元件进行积极的交换。这些发现表明，pipolins 和潜在的其他防御岛作为防御基因的正交库，可能可转移到免疫自主的 MGEs 中，这表明了细菌种群中防御基因的互补交换机制。
