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Updated: May 23, 2025

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AcrDB更新:预测人类肠道病毒组中的反CRISPRs的3D结构

Minal Khatri¹, N R Siva Shanmugam¹, Xinpeng Zhang¹

¹Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.

Protein science : a publication of the Protein Society

|May 22, 2025

概括

这项研究引入了更新的Anti-CRISPR数据库 (AcrDB),其中包括来自肠道病毒的预测结构和新的结构搜索功能. 它确定了795个候选Acrs,推动了基因组编辑和菌体与宿主相互作用研究.

科学领域:

基因组学和生物信息学
分子生物学分子生物学
结构生物学结构生物学

背景情况:

反CRISPR (Acr) 蛋白在菌体与宿主相互作用中至关重要,并有可能用于基因组编辑.
由于序列相似性较低,发现新型Acrs受到阻碍,需要使用替代的识别方法.
蛋白质结构预测的进步为Acr通过结构比较的发现提供了新的途径.

研究的目的:

更新和增强Anti-CRISPR数据库 (AcrDB) 以新的功能来改进Acr发现.
使用先进的结构预测工具,从人类肠道病毒组中预测和识别候选Acrs.
开发一个结构相似性搜索功能,以识别基于3D结构的新Acrs.

主要方法:

利用AlphaFold2从肠道病毒组数据库预测候选Acrs的3D结构.
实现基于非序列相似性的工具 (TM-Vec,Foldseek,AcrPred) 用于与已知的Acrs进行结构比较.
执行了基于序列和结构的集群,以对已识别的Acr进行分类并分析关系.

主要成果:

更新的AcrDB包括795名候选Acrs的预测结构,其中121名候选人高度自信.
确定了44个候选Acr家族和119个已知的Acr家族之间的结构相似性.
发现,鉴定的Acrs的细菌宿主主要来自主导性肠道类 (Bacillota,Pseudomonadota,Bacteroidota).

结论:

增强的AcrDB为发现新型Anti-CRISPR蛋白质提供了宝贵的资源,特别是来自人类肠道微生物群.
结构相似性搜索有助于识别基于序列的方法遗漏的Acrs.
这些发现突显了肠道细菌群体内ACRS的流行率和潜在重要性,用于菌体防御和生物技术应用.

关键词:

这就是CRISPR-Cas.这是一个反CRISPR的方法.对抗防御基因的基因.细菌免疫力细菌免疫力结构相似性结构相似性病毒组病毒组

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