As part of the ongoing bacterial-phage arms race, CRISPR-Cas systems in bacteria clear invading phages whereas anti-CRISPR proteins (Acrs) in phages inhibit CRISPR defenses. Known Acrs have proven extremely diverse, complicating their identification. Here, we report a deep learning algorithm for Acr identification that revealed an Acr against type VI-B CRISPR-Cas systems. The algorithm predicted numerous putative Acrs spanning almost all CRISPR-Cas types and subtypes, including over 7,000 putative type IV and VI Acrs not predicted by other algorithms. By performing a cell-free screen for Acr hits against type VI-B systems, we identified a potent inhibitor of Cas13b nucleases we named AcrVIB1. AcrVIB1 blocks Cas13b-mediated defense against a targeted plasmid and lytic phage, and its inhibitory function principally occurs upstream of ribonucleoprotein complex formation. Overall, our work helps expand the known Acr universe, aiding our understanding of the bacteria-phage arms race and the use of Acrs to control CRISPR technologies.

作为正在进行的细菌噬菌体军备竞赛的一部分，细菌中的 CRISPR-Cas 系统清除入侵的噬菌体，而噬菌体中的抗 CRISPR 蛋白 (Acrs) 抑制 CRISPR 防御。已知 Acrs 已被证明极其多样化，使它们的识别变得复杂。在这里，我们报告了一种用于 Acr 识别的深度学习算法，该算法揭示了针对 VI-B 型 CRISPR-Cas 系统的 Acr。该算法预测了几乎所有 CRISPR-Cas 类型和亚型的众多推定 Acrs，包括其他算法无法预测的 7,000 多个推定的 IV 型和 VI 型 Acrs。通过对针对 VI-B 型系统的 Acr 命中进行无细胞筛选，我们确定了一种有效的 Cas13b 核酸酶抑制剂，我们将其命名为 AcrVIB1。AcrVIB1 阻断 Cas13b 介导的针对靶向质粒和裂解噬菌体的防御，其抑制功能主要发生在核糖核蛋白复合物形成的上游。总体而言，我们的工作有助于扩展已知的 Acr 宇宙，帮助我们了解细菌-噬菌体军备竞赛以及使用 Acrs 来控制 CRISPR 技术。