CRISPR defense systems such as the well-known DNA-targeting Cas9 and the RNA-targeting type III systems are widespread in prokaryotes^1,2. The latter can orchestrate a complex antiviral response that is initiated by the synthesis of cyclic oligoadenylates (cOAs) upon foreign RNA recognition^3–5. Among a large set of proteins that were linked to type III systems and predicted to bind cOAs^6,7, a CRISPR associated Lon protease (CalpL) stood out to us. The protein contains a sensor domain of the SAVED (SMODS-associated and fused to various effector domains) family⁷, fused to a Lon protease effector domain. However, the mode of action of this effector was unknown. Here, we report the structure and function of CalpL and show that the soluble protein forms a stable tripartite complex with two further proteins, CalpT and CalpS, that are encoded in the same operon. Upon activation by cA₄, CalpL oligomerizes and specifically cleaves the MazF-homolog CalpT, releasing the extracytoplasmic function (ECF) sigma factor CalpS from the complex. This provides a direct connection between CRISPR-based foreign nucleic acid detection and transcriptional regulation. Furthermore, the presence of a cA₄-binding SAVED domain in a CRISPR effector reveals an unexpected link to the cyclic oligonucleotide-based antiphage signaling system (CBASS).

CRISPR 防御系统，例如众所周知的 DNA 靶向 Cas9 和 RNA 靶向 III 型系统，在原核生物中广泛存在^1,2。后者可以协调复杂的抗病毒反应，该反应是由外来 RNA 识别后合成环状寡腺苷酸 (cOA) 启动的^3-5。^{在与 III 型系统相关并预计能结合 cOA 6,7 的}大量蛋白质中，CRISPR 相关的 Lon 蛋白酶 (CalpL) 对我们脱颖而出。该蛋白含有 SAVED（SMODS 相关并与各种效应结构域融合）家族⁷的传感器结构域，与 Lon 蛋白酶效应结构域融合。然而，该效应器的作用方式尚不清楚。在这里，我们报告了 CalpL 的结构和功能，并表明可溶性蛋白与同一操纵子中编码的另外两种蛋白 CalpT 和 CalpS 形成稳定的三方复合物。被 cA ₄激活后，CalpL 寡聚化并特异性裂解 MazF 同源物 CalpT，从复合物中释放胞质外功能 (ECF) σ 因子 CalpS。这提供了基于 CRISPR 的外源核酸检测和转录调控之间的直接联系。此外， CRISPR效应子中cA ₄结合SAVED结构域的存在揭示了与基于环状寡核苷酸的抗噬菌体信号系统（CBASS）的意外联系。