Understanding the nature of anti-phage defense islands in microbes

细菌参与了一场持续的军备竞赛，它们试图保护自己免受快速进化的噬菌体的攻击。为此，细菌进化出了专门的防御系统，包括限制性修饰、CRISPR-Cas、流产感染和大量其他防御系统。对细菌和古细菌基因组的分析表明，防御系统在微生物基因组中非随机分布，并聚集在称为“防御岛”的特定基因组位置。防御系统的这一特性使得许多新的抗噬菌体防御系统基于它们在限制系统、CRISPR-Cas和其他已知的多种微生物基因组防御系统附近的优先基因组定位得以预测和后来的实验验证。虽然防御岛的概念有助于最近发现许多防御系统，但防御岛本身的性质仍然含糊不清。什么是防御岛？防御岛的定义是什么？防御岛是否涉及在微生物基因组之间转移防御系统？如果有，怎么做？它们在微生物基因组中出现的频率是多少？这些问题目前完全没有答案，将在当前拟议的项目中解决。作为我们未发表的初步结果的一部分，我们开发了一种方法，可以确定微生物基因组中防御岛的确切边界。通过这些数据，我们发现了初步证据，表明一些防御岛是专门用于在基因组之间携带和动员防御系统的移动遗传元件。在当前的提案中，我们提出了一个综合计算/实验计划，以全面绘制大量微生物基因组中的防御岛，了解它们的内容，整合模式和基因组之间的迁移。这将使我们了解防御岛如何在基因组之间传播噬菌体抗性特征，并进一步发现迄今为止未被发现的抗噬菌体防御系统的新家族。

Bacteria are engaged in a continuous arms race in which they seek to defend themselves against rapidly evolving phages. To this end, bacteria evolved dedicated defense systems, including restriction-modification, CRISPR-Cas, abortive infection, and a large diversity of additional defense systems. Analysis of bacterial and archaeal genomes have shown that defense systems are non-randomly distributed in microbial genomes, and are clustered to specific genomic locations that were termed “defense islands”. This property of defense systems allowed the prediction, and later the experimental verification, of numerous novel anti-phage defense systems based on their preferential genomic localization near restriction systems, CRISPR-Cas, and other known defense systems in multiple microbial genomes. Although the concept of defense islands have been instrumental for the recent discovery of many defense systems, the nature of defense islands themselves remained vague. What are defense islands? What defines a defense island? Are defense islands involved in transferring defense systems between microbial genomes? If so, how? How often do they appear in microbial genomes? These questions are currently completely unanswered and will be addressed in the current proposed project. As part of our preliminary, unpublished results, we developed methodologies that allow to identify the exact boundaries of defense islands within the microbial genome. With these data, we found preliminary evidence suggesting that some defense islands are mobile genetic elements dedicated for carrying and mobilizing defense systems between genomes. In the current proposal we present a combined computational/experimental plan to comprehensively map defense islands in a large set of microbial genomes, understand their content, integration patterns, and mobility between genomes. This will allow us to understand how defense islands spread phage resistance traits between genomes, and furthermore to discover new families of anti-phage defense systems that so far escaped detection.