a Department of Biochemistry , University of Otago , Dunedin , New Zealand.
b Genetics Otago , University of Otago , Dunedin , New Zealand.
RNA Biol. 2019 Apr;16(4):566-576. doi: 10.1080/15476286.2018.1509662. Epub 2018 Sep 18.
CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against invading genetic elements, such as plasmids, bacteriophages and archaeal viruses. They consist of cas genes and CRISPR loci, which store genetic memories of previously encountered invaders as short sequences termed spacers. Spacers determine the specificity of CRISPR-Cas defence and immunity can be gained or updated by the addition of new spacers into CRISPR loci. There are two main routes to spacer acquisition, which are known as naïve and primed CRISPR adaptation. Naïve CRISPR adaptation involves the de novo formation of immunity, independent of pre-existing spacers. In contrast, primed CRISPR adaptation (priming) uses existing spacers to enhance the acquisition of new spacers. Priming typically results in spacer acquisition from locations near the site of target recognition by the existing (priming) spacer. Primed CRISPR adaptation has been observed in several type I CRISPR-Cas systems and it is potentially widespread. However, experimental evidence is unavailable for some subtypes, and for most systems, priming has only been shown in a small number of hosts. There is also no current evidence of priming by other CRISPR-Cas types. Here, we used a bioinformatic approach to search for evidence of priming in diverse CRISPR-Cas systems. By analysing the clustering of spacers acquired from phages, prophages and archaeal viruses, including strand and directional biases between subsequently acquired spacers, we demonstrate that two patterns of primed CRISPR adaptation dominate in type I systems. In addition, we find evidence of a priming-like pathway in type II CRISPR-Cas systems.
CRISPR-Cas 系统为细菌和古菌提供了针对入侵遗传元件（如质粒、噬菌体和古菌病毒）的适应性免疫。它们由 cas 基因和 CRISPR 基因座组成，CRISPR 基因座将先前遇到的入侵物的遗传记忆作为短序列（称为间隔子）存储。间隔子决定了 CRISPR-Cas 防御的特异性，并且可以通过将新的间隔子添加到 CRISPR 基因座中来获得或更新免疫性。有两种主要的获取间隔子的途径，分别称为原始和诱导 CRISPR 适应。原始 CRISPR 适应涉及独立于先前存在的间隔子的新免疫的形成。相比之下，诱导 CRISPR 适应（引发）使用现有的间隔子来增强新间隔子的获取。引发通常导致在现有（引发）间隔子的靶标识别位点附近的位置获取新的间隔子。已经在几种 I 型 CRISPR-Cas 系统中观察到诱导 CRISPR 适应，并且它可能广泛存在。然而，一些亚类缺乏实验证据，并且对于大多数系统，仅在少数宿主中显示了引发。目前也没有其他 CRISPR-Cas 类型引发的证据。在这里，我们使用生物信息学方法来搜索不同 CRISPR-Cas 系统中引发的证据。通过分析从噬菌体、前噬菌体和古菌病毒中获得的间隔子的聚类，包括随后获得的间隔子之间的链和方向偏向，我们表明两种 I 型系统的诱导 CRISPR 适应模式占主导地位。此外，我们在 II 型 CRISPR-Cas 系统中发现了类似于引发的途径的证据。
