Clustered regularly interspaced short palindromic repeats (CRISPR)–Cas systems are prokaryotic adaptive immune systems against invading phages and other mobile genetic elements. Notably, some phages, including the Vibrio cholerae-infecting ICP1 (International Center for Diarrheal Disease Research, Bangladesh cholera phage 1), harbor CRISPR–Cas systems to counteract host defenses. Nevertheless, ICP1 Cas8f lacks the helical bundle domain essential for recruitment of helicase-nuclease Cas2/3 during target DNA cleavage and how this system accomplishes the interference stage remains unknown. Here, we found that Cas1, a highly conserved component known to exclusively work in the adaptation stage, also mediates the interference stage through connecting Cas2/3 to the DNA-bound CRISPR-associated complex for antiviral defense (Cascade; CRISPR system yersinia, Csy) of the ICP1 CRISPR–Cas system. A series of structures of Csy, Csy–dsDNA (double-stranded DNA), Cas1–Cas2/3 and Csy–dsDNA–Cas1–Cas2/3 complexes reveal the whole process of Cas1-mediated target DNA cleavage by the ICP1 CRISPR–Cas system. Together, these data support an unprecedented model in which Cas1 mediates the interference stage in a phage-encoded CRISPR–Cas system and the study also sheds light on a unique model of primed adaptation.

成簇的规则间隔短回文重复序列 （CRISPR）-Cas 系统是针对入侵噬菌体和其他移动遗传元件的原核适应性免疫系统。值得注意的是，一些噬菌体，包括感染霍乱弧菌的 ICP1（国际腹泻病研究中心，孟加拉国霍乱噬菌体 1），含有 CRISPR-Cas 系统以对抗宿主防御。然而，ICP1 Cas8f 缺乏在靶 DNA 切割过程中募集解旋酶核酸酶 Cas2/3 所必需的螺旋束结构域，该系统如何完成干扰阶段仍然未知。在这里，我们发现 Cas1 是一种已知仅在驯化阶段起作用的高度保守的成分，它也通过将 Cas2/3 连接到 DNA 结合的 CRISPR 相关复合物来介导干扰阶段以进行抗病毒防御（级联;ICP1 CRISPR-Cas 系统的 CRISPR 系统 yersinia， Csy）。Csy、Csy-dsDNA（双链 DNA）、Cas1-Cas2/3 和 Csy-dsDNA-Cas1-Cas2/3 复合物的一系列结构揭示了 ICP1 CRISPR-Cas 系统切割 Cas1 介导的靶 DNA 的整个过程。总之，这些数据支持了一个前所未有的模型，其中 Cas1 介导噬菌体编码的 CRISPR-Cas 系统中的干扰阶段，并且该研究还阐明了一种独特的引物适应模型。