Department of Genetics, University of North Carolina at Chapel Hill, NC, USA.
Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln, Lincoln, NE 68588, USA.
Nucleic Acids Res. 2021 Jan 8;49(D1):D622-D629. doi: 10.1093/nar/gkaa857.
CRISPR-Cas is an anti-viral mechanism of prokaryotes that has been widely adopted for genome editing. To make CRISPR-Cas genome editing more controllable and safer to use, anti-CRISPR proteins have been recently exploited to prevent excessive/prolonged Cas nuclease cleavage. Anti-CRISPR (Acr) proteins are encoded by (pro)phages/(pro)viruses, and have the ability to inhibit their host's CRISPR-Cas systems. We have built an online database AcrDB (http://bcb.unl.edu/AcrDB) by scanning ∼19 000 genomes of prokaryotes and viruses with AcrFinder, a recently developed Acr-Aca (Acr-associated regulator) operon prediction program. Proteins in Acr-Aca operons were further processed by two machine learning-based programs (AcRanker and PaCRISPR) to obtain numerical scores/ranks. Compared to other anti-CRISPR databases, AcrDB has the following unique features: (i) It is a genome-scale database with the largest collection of data (39 799 Acr-Aca operons containing Aca or Acr homologs); (ii) It offers a user-friendly web interface with various functions for browsing, graphically viewing, searching, and batch downloading Acr-Aca operons; (iii) It focuses on the genomic context of Acr and Aca candidates instead of individual Acr protein family and (iv) It collects data with three independent programs each having a unique data mining algorithm for cross validation. AcrDB will be a valuable resource to the anti-CRISPR research community.
CRISPR-Cas 是原核生物的抗病毒机制，已被广泛应用于基因组编辑。为了使 CRISPR-Cas 基因组编辑更加可控和安全，最近利用抗 CRISPR 蛋白来防止 Cas 核酸酶过度/延长切割。抗 CRISPR（Acr）蛋白由（前）噬菌体/（前）病毒编码，具有抑制其宿主 CRISPR-Cas 系统的能力。我们使用最近开发的 Acr-Aca（Acr 相关调节剂）操纵子预测程序 AcrFinder，对大约 19000 个原核生物和病毒基因组进行扫描，构建了一个在线数据库 AcrDB（http://bcb.unl.edu/AcrDB）。Acr-Aca 操纵子中的蛋白进一步通过两个基于机器学习的程序（AcRanker 和 PaCRISPR）进行处理，以获得数值评分/等级。与其他抗 CRISPR 数据库相比，AcrDB 具有以下独特特征：（i）它是一个基因组规模的数据库，拥有最大的数据集合（39799 个包含 Aca 或 Acr 同源物的 Acr-Aca 操纵子）；（ii）它提供了一个用户友好的 Web 界面，具有各种浏览、图形查看、搜索和批量下载 Acr-Aca 操纵子的功能；（iii）它专注于 Acr 和 Aca 候选物的基因组背景，而不是单个 Acr 蛋白家族；（iv）它使用三个独立的程序收集数据，每个程序都具有独特的数据挖掘算法进行交叉验证。AcrDB 将成为抗 CRISPR 研究界的宝贵资源。
