碱基编辑器的开发及其在细菌基因组编辑中的应用

碱基编辑器是近两年发展起来的新型基因组编辑工具,它将碱基脱氨酶的催化活性和CRISPR/Cas系统的靶向特异性进行结合,催化DNA或RNA链上特定位点的碱基发生脱氨基反应,进而完成碱基的替换。碱基编辑器分为DNA和RNA碱基编辑器两大类,其中DNA碱基编辑器分为两种:胞嘧啶碱基编辑器和腺嘌呤碱基编辑器;前者可以实现胞嘧啶到胸腺嘧啶的转换,而后者则可以将腺嘌呤突变为鸟嘌呤。由于DNA碱基编辑器不会造成DNA的双链断裂(DSB),也不依赖于宿主的非同源末端修复和同源重组途径,因此,大大减少了DSB相关的编辑副产物,如小片段插入或缺失等。基于CRISPR/Cas系统的RNA碱基编辑器,可以实现RNA链上腺嘌呤核苷到次黄苷的转换。本文对不同类型碱基编辑器的开发过程、适用范围和编辑特点等进行梳理,并对其在细菌基因组编辑中的应用进行了介绍;最后简要探讨了细菌中碱基编辑器的缺点以及将来可能的研究方向。

Development and application of base editors in bacterial genome editing

Base editors are novel genome-editing tools developed in the past two years that comprise fusions between a catalytically disabled CRISPR/Cas endonuclease and a base deaminase to deaminate the exocyclic amine of the target bases, thereby leading to base substitutions in DNA or RNA. Two classes of base editors have been developed, namely DNA base editors and RNA base editors. Two types of DNA editors have been described: cytosine base editors (CBEs) convert C to T and adenine base editors (ABEs) convert A to G. Base editors do not create double-strand DNA breaks (DSBs) and do not rely on cellular non-homologous end joining (NHEJ) and homology-directed repair (HDR), so they minimize the generation of DSB-associated by products, such as small insertions or deletion (indels). RNA base editors based on CRISPR/Cas systems could achieve adenosine conversion to inosine. In this review, we summarize the development process, scope of application and editing features of base editors and highlight their recent applications in bacterial genome editing. Finally, we will also briefly discuss limitations and future directions of base editors for applications in bacteria.