Abstract

Cytidine and adenosine deaminases are required for cytosine and adenine editing of base editors respectively, and no single deaminase could enable concurrent and comparable cytosine and adenine editing. Additionally, distinct properties of cytidine and adenosine deaminases lead to various types of off-target effects, including Cas9-indendepent DNA off-target effects for cytosine base editors (CBEs) and RNA off-target effects particularly severe for adenine base editors (ABEs). Here we demonstrate that 25 TadA orthologs could be engineered to generate functional ABEs, CBEs or ACBEs via single or double mutations, which display minimized Cas9-independent DNA off-target effects and genotoxicity, with orthologs B5ZCW4, Q57LE3, E8WVH3, Q13XZ4 and B3PCY2 as promising candidates for further engineering. Furthermore, RNA off-target effects of TadA ortholog-derived base editors could be further reduced or even eliminated by additional single mutation. Taken together, our work expands the base editing toolkits, and also provides important clues for the potential evolutionary process of deaminases.

Properties of cytidine and adenosine deaminases lead to off-target effects for cytosine base editors (CBEs) and adenine base editors (ABEs). Here the authors report that 25 TadA orthologs could be engineered to generate functional ABEs, CBEs or ACBEs via single/double mutations with minimised off-targets.

Details

Title
TadA orthologs enable both cytosine and adenine editing of base editors
Author
Zhang, Shuqian 1 ; Yuan, Bo 2   VIAFID ORCID Logo  ; Cao, Jixin 3 ; Song, Liting 3 ; Chen, Jinlong 4 ; Qiu, Jiayi 4 ; Qiu, Zilong 5   VIAFID ORCID Logo  ; Zhao, Xing-Ming 6   VIAFID ORCID Logo  ; Chen, Jingqi 6   VIAFID ORCID Logo  ; Cheng, Tian-Lin 4   VIAFID ORCID Logo 

1  Fudan University, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institute of Pediatrics, National Children’s Medical Center, Children’s Hospital, Shanghai, China (GRID:grid.8547.e) (ISNI:0000 0001 0125 2443); Qilu Hospital of Shandong University, Department of Pediatrics, Ji’nan, China (GRID:grid.452402.5) (ISNI:0000 0004 1808 3430) 
2  CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Institute of Neuroscience, State Key Laboratory of Neuroscience, Shanghai, China (GRID:grid.9227.e) (ISNI:0000000119573309) 
3  Fudan University, Institute of Science and Technology for Brain-Inspired Intelligence, Shanghai, China (GRID:grid.8547.e) (ISNI:0000 0001 0125 2443) 
4  Fudan University, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institute of Pediatrics, National Children’s Medical Center, Children’s Hospital, Shanghai, China (GRID:grid.8547.e) (ISNI:0000 0001 0125 2443) 
5  CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Institute of Neuroscience, State Key Laboratory of Neuroscience, Shanghai, China (GRID:grid.9227.e) (ISNI:0000000119573309); Fudan University, National Clinical Research Center for Aging and Medicine, Huashan Hopsital, Shanghai, China (GRID:grid.8547.e) (ISNI:0000 0001 0125 2443); Shanghai Jiao Tong University School of Medicine, Songjiang Hospital, Songjiang Institute, Shanghai, China (GRID:grid.16821.3c) (ISNI:0000 0004 0368 8293) 
6  Fudan University, Institute of Science and Technology for Brain-Inspired Intelligence, Shanghai, China (GRID:grid.8547.e) (ISNI:0000 0001 0125 2443); Fudan University, State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Shanghai, China (GRID:grid.8547.e) (ISNI:0000 0001 0125 2443); Fudan University, MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Shanghai, China (GRID:grid.8547.e) (ISNI:0000 0001 0125 2443) 
Pages
414
Publication year
2023
Publication date
2023
Publisher
Nature Publishing Group
e-ISSN
20411723
Source type
Scholarly Journal
Language of publication
English
DOI
https://doi.org/10.1038/s41467-023-36003-3
ProQuest document ID
2769875020
Copyright
© The Author(s) 2023. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.