National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MD 20894, USA.
J Bacteriol. 2011 Nov;193(21):6039-56. doi: 10.1128/JB.05535-11. Epub 2011 Sep 9.
The arms race between cellular life forms and viruses is a major driving force of evolution. A substantial fraction of bacterial and archaeal genomes is dedicated to antivirus defense. We analyzed the distribution of defense genes and typical mobilome components (such as viral and transposon genes) in bacterial and archaeal genomes and demonstrated statistically significant clustering of antivirus defense systems and mobile genes and elements in genomic islands. The defense islands are enriched in putative operons and contain numerous overrepresented gene families. A detailed sequence analysis of the proteins encoded by genes in these families shows that many of them are diverged variants of known defense system components, whereas others show features, such as characteristic operonic organization, that are suggestive of novel defense systems. Thus, genomic islands provide abundant material for the experimental study of bacterial and archaeal antivirus defense. Except for the CRISPR-Cas systems, different classes of defense systems, in particular toxin-antitoxin and restriction-modification systems, show nonrandom clustering in defense islands. It remains unclear to what extent these associations reflect functional cooperation between different defense systems and to what extent the islands are genomic "sinks" that accumulate diverse nonessential genes, particularly those acquired via horizontal gene transfer. The characteristics of defense islands resemble those of mobilome islands. Defense and mobilome genes are nonrandomly associated in islands, suggesting nonadaptive evolution of the islands via a preferential attachment-like mechanism underpinned by the addictive properties of defense systems such as toxins-antitoxins and an important role of horizontal mobility in the evolution of these islands.
细胞生命形式与病毒之间的军备竞赛是进化的主要驱动力。大量的细菌和古菌基因组专门用于抗病毒防御。我们分析了细菌和古菌基因组中防御基因和典型移动元件（如病毒和转座子基因）的分布，并证明了抗病毒防御系统和移动基因和元件在基因组岛中存在统计学上显著的聚类。防御岛富含假定的操纵子，并且包含许多过表达的基因家族。对这些家族中基因编码的蛋白质进行详细的序列分析表明，其中许多是已知防御系统成分的分化变体，而其他则具有特征，例如特征性操纵子组织，暗示存在新的防御系统。因此，基因组岛为细菌和古菌抗病毒防御的实验研究提供了丰富的材料。除了 CRISPR-Cas 系统外，不同类别的防御系统，特别是毒素-抗毒素和限制-修饰系统，在防御岛中表现出非随机聚类。这些关联在多大程度上反映了不同防御系统之间的功能合作，以及岛屿在多大程度上是积累各种非必需基因的基因组“汇”，特别是那些通过水平基因转移获得的基因，这一点尚不清楚。防御岛的特征与移动元件岛的特征相似。防御和移动基因在岛屿中随机关联，表明岛屿通过类似于优先附着的机制进行非适应性进化，这种机制由毒素-抗毒素等防御系统的附加性质以及水平移动在这些岛屿进化中的重要作用所支撑。
