DddA homolog search and engineering expand sequence compatibility of mitochondrial base editing

• Published in: Nature communications Vol. 14; no. 1; p. 874
• Main Authors: Mi, Li, Shi, Ming, Li, Yu-Xuan, Xie, Gang, Rao, Xichen, Wu, Damu, Cheng, Aimin, Niu, Mengxiao, Xu, Fengli, Yu, Ying, Gao, Ning, Wei, Wensheng, Wang, Xianhua, Wang, Yangming
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 16.02.2023; Nature Publishing Group; Nature Portfolio
• Subjects: 13/106; 13/109; 13/44; 14; 42; 45; 45/22; 45/23; 45/77; 631/1647/1513; 631/337/4041/3196; 631/61/338; 82/29; Amino acid substitution; Amino acids; Compatibility; Context; CRISPR-Cas Systems; Cytosine; DNA, Mitochondrial - genetics; Editing; Gene Editing; Homology; Humanities and Social Sciences; Mitochondria - genetics; Mitochondrial DNA; multidisciplinary; Mutation; Science; Science (multidisciplinary); Therapeutic applications
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-023-36600-2

Expanding mitochondrial base editing tools with broad sequence compatibility is of high need for both research and therapeutic purposes. In this study, we identify a DddA homolog from Simiaoa sunii (Ddd_Ss) which can efficiently deaminate cytosine in D C context in double-stranded DNA (dsDNA). We successfully develop Ddd_Ss-derived cytosine base editors (DdCBE_Ss) and introduce mutations at multiple mitochondrial DNA (mtDNA) loci including disease-associated mtDNA mutations in previously inaccessible G C context. Finally, by introducing a single amino acid substitution from Ddd_Ss, we successfully improve the activity and sequence compatibility of DdCBE derived from DddA of Burkholderia cenocepacia (DdCBE_Bc). Our study expands mtDNA editing tool boxes and provides resources for further screening and engineering dsDNA base editors for biological and therapeutic applications. There is a need to improve and expand mitochondrial base editing tools. Here the authors identify a DddA homolog from Simiaoa sunii (Ddd_Ss) which can efficiently deaminate cytosine in dsDNA; they develop cytosine base editors and introduce mutations at multiple mitochondrial DNA loci.