Base editing technology and its application in microbial synthetic biology

WANG Yannan; SUN Yuhui

doi:10.12211/2096-8280.2022-053

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Base editing technology and its application in microbial synthetic biology

Invited Review | 更新时间：2025-03-20

- Base editing technology and its application in microbial synthetic biology
- Synthetic Biology Journal Vol. 4, Issue 4, Pages: 720-737(2023)
- 作者机构：
  
  武汉大学药学院，组合生物合成与新药发现教育部重点实验室，湖北武汉 430071
- 作者简介：
- 基金信息：
- DOI：10.12211/2096-8280.2022-053
  CLC： Q812
- Received：28 September 2022，
  
  Revised：2022-11-13，
  
  Published：31 August 2023
- 稿件说明：
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王雁南，孙宇辉. 碱基编辑技术及其在微生物合成生物学中的应用［J］. 合成生物学， 2023， 4（4）： 720-737

WANG Yannan， SUN Yuhui. Base editing technology and its application in microbial synthetic biology［J］. Synthetic Biology Journal， 2023， 4（4）： 720-737
王雁南，孙宇辉. 碱基编辑技术及其在微生物合成生物学中的应用［J］. 合成生物学， 2023， 4（4）： 720-737 DOI： 10.12211/2096-8280.2022-053.

WANG Yannan， SUN Yuhui. Base editing technology and its application in microbial synthetic biology［J］. Synthetic Biology Journal， 2023， 4（4）： 720-737 DOI： 10.12211/2096-8280.2022-053.

摘要

CRISPR/Cas系统的发现与发展对生命科学领域产生了革命性的影响，借助CRISPR/Cas系统研发出的一系列工具为相关领域的研究带来了极大的便利。碱基编辑器便是其中一类基于CRISPR/Cas系统开发的可实现碱基转换和颠换的基因编辑工具，其通过将胞苷或腺苷脱氨酶以及其他功能元件与失去双链切割活性的Cas蛋白相融合，由sgRNA引导，实现对基因组上目标位置胞嘧啶或腺嘌呤的碱基转换。碱基编辑器一经开发便在生物学、医学等领域展现出巨大的应用潜力，虽然经过不断优化，但目前在使用时仍然存在着许多制约因素。本文简述了几种主要碱基编辑器的发展，并介绍了碱基编辑器存在的靶向范围受限和脱靶编辑的问题以及现有的优化措施。同时列举了我国部分科研工作者将碱基编辑技术运用于微生物合成生物学领域的进展，并展望了碱基编辑技术的发展及其在微生物合成生物学领域的应用前景。

Abstract

The discovery and development of the CRISPR/Cas system have a revolutionary influence on life sciences. A series of tools derived from the CRISPR/Cas system have brought great convenience to research in the field of life sciences. The base editors developed based on the CRISPR/Cas system are gene editing tools that can achieve base conversions and transversion on target. The base editors are constructed by fusing cytosine or adenosine deaminase

and other functional elements to Cas proteins with abolished double strand DNA cleavage activity to convert cytidine or adenine into other bases at genome on-target sites guided by sgRNAs. Base editors have shown great potential in biology

medicine and related fields. Although they have already been continuously optimized

there are still problems affecting further application of base editors. In this review

we briefly describe the development of DNA base editors. Furthermore

we introduce in detail the problems of the limited editing range of base editors as well as the corresponding optimization strategies by increasing the target sites recognized by the locator moiety and expanding or narrowing the editing window of the effector moiety. At the same time

we introduce several off-target editing detection methods specially developed for base editing. Based on usual and developed detection methods

multiple and frequent off-target editing caused by base editors were found at both DNA and RNA levels. We also introduced various effective optimization strategies to improve the editing specificity of the base editors in every respect. Most of these strategies are based on protein modification

but also on optimization of sgRNA and spatio-temporal regulation of base editing systems. These measures greatly enrich the application scenarios of the base editors. Then

we discuss the progress on applying base editors to the field of microbial synthetic biology

including revealing the metabolic pathway and synthesis mechanism of natural products as well as improving the production of target compounds in multiple species. Finally

we envisage the promising development of base editing in synthetic biology in the future.

关键词

Keywords

references

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