PDF(Pubmed)
Abstract：
In silico identification of viral anti-CRISPR proteins (Acrs) has relied largely on the guilt-by-association method using known Acrs or anti-CRISPR associated proteins (Acas) as the bait. However, the low number and limited spread of the characterized archaeal Acrs and Aca hinders our ability to identify Acrs using guilt-by-association. Here, based on the observation that the few characterized archaeal Acrs and Aca are transcribed immediately post viral infection, we hypothesize that these genes, and many other unidentified anti-defense genes (ADG), are under the control of conserved regulatory sequences including a strong promoter, which can be used to predict anti-defense genes in archaeal viruses. Using this consensus sequence based method, we identify 354 potential ADGs in 57 archaeal viruses and 6 metagenome-assembled genomes. Experimental validation identified a CRISPR subtype I-A inhibitor and the first virally encoded inhibitor of an archaeal toxin-antitoxin based immune system. We also identify regulatory proteins potentially akin to Acas that can facilitate further identification of ADGs combined with the guilt-by-association approach. These results demonstrate the potential of regulatory sequence analysis for extensive identification of ADGs in viruses of archaea and bacteria.
摘要：
病毒抗CRISPR蛋白（Acrs）的计算机识别在很大程度上依赖于使用已知Acrs或抗CRISPR相关蛋白（Acas）作为诱饵的罪恶感关联方法。然而,具有特征的古细菌Acrs和Aca的数量少和传播有限，阻碍了我们使用内感来识别Acrs的能力。这里,根据观察，少数特征的古细菌Acrs和Aca在病毒感染后立即转录，我们假设这些基因，和许多其他未知的抗防御基因（ADG），受保守调控序列的控制，包括强启动子，可用于预测古细菌病毒中的抗防御基因。使用这种基于共有序列的方法，我们在57个古细菌病毒和6个宏基因组组装的基因组中鉴定了354个潜在的ADGs.实验验证鉴定了CRISPR亚型I-A抑制剂和基于古细菌毒素-抗毒素的免疫系统的第一个病毒编码抑制剂。我们还鉴定了可能类似于Acas的调节蛋白，这些蛋白可以促进与关联罪恶感方法相结合的ADG的进一步鉴定。这些结果证明了调控序列分析在古细菌和细菌病毒中广泛鉴定ADG的潜力。
