Khatri Minal, Shanmugam N R Siva, Zhang Xinpeng, Patel Revanth Sai Kumar Reddy, Yin Yanbin
Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.
Protein Sci. 2025 Jun;34(6):e70177. doi: 10.1002/pro.70177.
Anti-CRISPR (Acr) proteins play a key role in phage-host interactions and hold great promise for advancing genome-editing technologies. However, finding new Acrs has been challenging due to their low sequence similarity. Recent advances in protein structure prediction have opened new pathways for Acr discovery by using 3D structure similarity. This study presents an updated AcrDB, with the following new features not available in other databases: (1) predicted Acrs from human gut virome databases, (2) Acr structures predicted by AlphaFold2, (3) a structural similarity search function to allow users to submit new sequences and structures to search against 3D structures of experimentally known Acrs. The updated AcrDB contains predicted 3D structures of 795 candidate Acrs with structural similarity (TM-score ≥0.7) to known Acrs supported by at least two of the three non-sequence similarity-based tools (TM-Vec, Foldseek, AcrPred). Among these candidate Acrs, 121 are supported by all three tools. AcrDB also includes 3D structures of 122 experimentally characterized Acr proteins. The 121 most confident candidate Acrs were combined with the 122 known Acrs and clustered into 163 sequence similarity-based Acr families. The 163 families were further subject to a structure similarity-based hierarchical clustering, revealing structural similarity between 44 candidate Acr (cAcr) families and 119 known Acr families. The bacterial hosts of these 163 Acr families are mainly from Bacillota, Pseudomonadota, and Bacteroidota, which are all dominant gut bacterial phyla. Many of these 163 Acr families are also co-localized in Acr operons. All the data and visualization are provided on our website: https://pro.unl.edu/AcrDB.
抗CRISPR（Acr）蛋白在噬菌体 - 宿主相互作用中起关键作用，在推进基因组编辑技术方面具有巨大潜力。然而，由于它们的序列相似性低，寻找新的Acr一直具有挑战性。蛋白质结构预测的最新进展通过使用三维结构相似性为Acr发现开辟了新途径。本研究展示了一个更新的AcrDB，具有以下其他数据库中没有的新功能：（1）从人类肠道病毒组数据库预测的Acr，（2）由AlphaFold2预测的Acr结构，（3）结构相似性搜索功能，允许用户提交新序列和结构，以与实验已知Acr的三维结构进行比对。更新后的AcrDB包含795个候选Acr的预测三维结构，这些候选Acr与已知Acr具有结构相似性（TM分数≥0.7），并得到三种基于非序列相似性的工具（TM-Vec、Foldseek、AcrPred）中至少两种的支持。在这些候选Acr中，121个得到了所有三种工具的支持。AcrDB还包括122种经过实验表征的Acr蛋白的三维结构。将121个最可靠的候选Acr与122个已知Acr合并，并聚集成163个基于序列相似性的Acr家族。这163个家族进一步进行基于结构相似性的层次聚类，揭示了44个候选Acr（cAcr）家族与119个已知Acr家族之间的结构相似性。这163个Acr家族的细菌宿主主要来自芽孢杆菌门、假单胞菌门和拟杆菌门，它们都是肠道中的优势细菌门类。这163个Acr家族中的许多也共定位于Acr操纵子中。所有数据和可视化内容都在我们的网站上提供：https://pro.unl.edu/AcrDB 。
