PNAS:原噬菌体基因组帮助细菌适应环境

原噬菌体是细菌基因库的多样性的主要贡献者。它们的驯化组成部分被认为是赋予细菌参与分泌，防御，攻击和基因转移的分子系统。然而，关于噬菌体的进化机制和驯化程度仍然知之甚少。

法国巴斯德研究所微生物进化基因组学的研究人员在新研究中，采用比较基因组学，对大肠埃希氏菌与肠道沙门氏菌基因组内的原噬菌体的进化进行研究。

研究分析确定，存在300多种遗传的病毒基因组插入到了这些细菌的基因组，它们基本上是完整的，而且携带了为病毒功能编码的基因，这提示细菌常常吸收病毒基因组，而这种现象可能驱动着细菌的适应。

大多数的这样吸收组分阻止了细菌基因组的删除，因为它们是由新的原噬菌体进行类似的功能取代。这使得细菌基因组处于一个噬菌体衍生的适应性基因采集和亏损的不断变化状态中。

原文摘要：

Pervasive domestication of defective prophages by bacteria

Louis-Marie Bobay, Marie Touchon and Eduardo P. C. Rocha

Integrated phages (prophages) are major contributors to the diversity of bacterial gene repertoires. Domestication of their components is thought to have endowed bacteria with molecular systems involved in secretion, defense, warfare, and gene transfer. However, the rates and mechanisms of domestication remain unknown. We used comparative genomics to study the evolution of prophages within the bacterial genome. We identified over 300 vertically inherited prophages within enterobacterial genomes. Some of these elements are very old and might predate the split between Escherichia coli and Salmonella enterica. The size distribution of prophage elements is bimodal, suggestive of rapid prophage inactivation followed by much slower genetic degradation. Accordingly, we observed a pervasive pattern of systematic counterselection of nonsynonymous mutations in prophage genes. Importantly, such patterns of purifying selection are observed not only on accessory regions but also in core phage genes, such as those encoding structural and lysis components. This suggests that bacterial hosts select for phage-associated functions. Several of these conserved prophages have gene repertoires compatible with described functions of adaptive prophage-derived elements such as bacteriocins, killer particles, gene transfer agents, or satellite prophages. We suggest that bacteria frequently domesticate their prophages. Most such domesticated elements end up deleted from the bacterial genome because they are replaced by analogous functions carried by new prophages. This puts the bacterial genome in a state of continuous flux of acquisition and loss of phage-derived adaptive genes.

作者：生物帮