Bioinformatics Discovery of Anti-CRISPR Operons in Human Gut Microbiome

人类肠道微生物组中抗 CRISPR 操纵子的生物信息学发现

基本信息

批准号：
10636879
负责人：
Yanbin Yin
金额：
$ 18.3万
依托单位：
UNIVERSITY OF NEBRASKA LINCOLN
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-06-07 至 2025-05-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10636879
关键词：
Algorithms Animals Archaeal Genome Bacteria Bacteriophages Basic Science Bioinformatics Biotechnology Clustered Regularly Interspaced Short Palindromic Repeats Communicable Diseases Computer software Data Databases Development Engineering Enterococcus Family Frequencies Genes Genetic Transcription Genome Genome engineering Genomics Homologous Gene Human Iceberg Immune Listeria Machine Learning Methods Microbe Mining Molecular Nature Nucleic Acid Sequence Homology Operon Paper Plants Prokaryotic Cells Prophages Protein Family Proteins Proviruses Pseudomonas PubMed Publishing Reporting Running Scanning Sequence Homology Site Software Tools System Technology Training Variant Viral Viral Genome Virus Work applied biomedical research bioinformatics tool combat computer program data mining genome editing genome-wide gut microbiome inhibitor innovation markov model metagenome microbial new technology novel open source pathogenic bacteria programs success tool user-friendly virome web server web site

项目摘要

PROJECT SUMMARY Various bacterial CRISPR-Cas systems and their variants have been engineered and repurposed for gene editing in animals, plants, and microbes since 2013. However, the current CRISPR-Cas genome editing tools are not perfectly safe to use. This is primarily due to the lack of an effective brake system and the off-target effect that may create unwanted cuts in the genome. Different strategies are being developed to reduce off- target effect and make CRISPR-Cas safer to use. A fact often overshadowed by the great success of genome editing is that, in the microbial world, CRISPR-Cas is an adaptive anti-viral immune mechanism present in ~50% of bacterial and ~90% of archaeal genomes. As a counterstrategy, anti-CRISPRs are produced by viruses and proviruses, as an anti-anti-viral mechanism, to inhibit the CRISPR-Cas systems of their prokaryote hosts. Thus, as the naturally occurring inhibitors of CRISPR-Cas, anti-CRISPR (Acr) proteins have obvious advantages to be used for developing safer and more controllable CRISPR-Cas genome editing technologies. The objective of this project is to develop a genomic context-based tool (AOMiner) for bioinformatics data mining of new Acr operons in human gut microbiome and virome. The significances of this project include: (i) it will enhance the experimental characterization of new anti-CRISPRs, which is fundamental to the understanding of phage-host interactions, and further to the development of novel phage-based technologies to combat pathogenic bacteria and infectious diseases; (ii) it will deliver new open source computer programs and online databases to provide novel anti-CRISPR candidates to be exploited for building safer and more controllable CRISPR-Cas genome editing tools. We recently developed AcrFinder (http://bcb.unl.edu/AcrFinder/), a bioinformatics software package for automated discovery of Acr operons, primarily based on sequence homology search. However, its ability to identify new Acrs is limited because it is largely based on homology search. The innovation of this project is that AOMiner (http://bcb.unl.edu/AOMiner) will implement a genomic context-based algorithm focusing on discovery of new Acr operons instead of Acr proteins. Additionally, this project will be the first large-scale genome mining for Acrs operons from human gut microbiome and virome, which will be developed into a gutAO database (http://bcb.unl.edu/gutAO). In summary, this project will deliver a suite of bioinformatics software tools in the form of open-source computer programs and online databases to assist the characterization of novel anti-CRISPRs.

项目概要各种细菌 CRISPR-Cas 系统及其变体已被设计并重新用于基因自 2013 年以来，人们开始对动物、植物和微生物进行编辑。然而，目前的 CRISPR-Cas 基因组编辑工具使用起来并不完全安全。这主要是由于缺乏有效的制动系统和偏离目标造成的。可能会在基因组中造成不必要的切割的效应。正在制定不同的策略来减少靶向作用，使CRISPR-Cas使用更安全。一个经常被基因组编辑的巨大成功所掩盖的事实是，在微生物世界中，CRISPR-Cas 是一种适应性抗病毒免疫机制，存在于约 50% 的细菌和约 90% 的古细菌基因组中。作为反策略是，抗 CRISPR 由病毒和原病毒产生，作为一种抗病毒机制，抑制原核生物宿主的 CRISPR-Cas 系统。因此，作为天然存在的抑制剂 CRISPR-Cas、抗CRISPR（Acr）蛋白优势明显，可用于开发更安全、更高效的产品可控CRISPR-Cas基因组编辑技术。该项目的目标是开发一种用于生物信息学数据的基于基因组上下文的工具（AOMiner）在人类肠道微生物组和病毒组中挖掘新的 Acr 操纵子。本项目的意义包括：（一）它将增强新的抗 CRISPR 的实验表征，这对于了解噬菌体-宿主相互作用，并进一步开发基于噬菌体的新型技术对抗病原菌和传染病； (ii) 它将提供新的开源计算机程序和在线数据库，提供新型抗 CRISPR 候选药物，用于构建更安全、更安全的项目可控的 CRISPR-Cas 基因组编辑工具。我们最近开发了 AcrFinder (http://bcb.unl.edu/AcrFinder/)，这是一个生物信息学软件包 Acr 操纵子的自动发现，主要基于序列同源性搜索。然而，它的能力识别新的 Acrs 是有限的，因为它很大程度上基于同源搜索。本项目的创新点是 AOMiner (http://bcb.unl.edu/AOMiner) 将实现一种基于基因组上下文的算法，重点关注发现新的 Acr 操纵子而不是 Acr 蛋白。此外，该项目将是第一个大规模从人类肠道微生物组和病毒组中挖掘 Acrs 操纵子的基因组，这将被开发成 gutAO 数据库 (http://bcb.unl.edu/gutAO)。总之，该项目将以开源的形式提供一套生物信息学软件工具计算机程序和在线数据库可帮助表征新型抗 CRISPR。