Characterization and development of a plastid genome base editor, ptpTALECD

SUMMARY The modification of photosynthesis‐related genes in plastid genomes may improve crop yields. Recently, we reported that a plastid‐targeting base editor named ptpTALECD, in which a cytidine deaminase DddA functions as the catalytic domain, can homoplasmically substitute a targeted C to T in p...

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Published in:The Plant journal : for cell and molecular biology 2023-08, Vol.115 (4), p.1151-1162
Main Authors: Nakazato, Issei, Okuno, Miki, Itoh, Takehiko, Tsutsumi, Nobuhiro, Arimura, Shin‐ichi
Format: Article
Language:English
Subjects:
Amino acid sequence
Amino acids
Arabidopsis
Arabidopsis thaliana
base editing
Chlorophyll
Crop yield
Cytidine deaminase
Genomes
Photosynthesis
plastid genome
Substitutes
technical advance
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Summary:SUMMARY The modification of photosynthesis‐related genes in plastid genomes may improve crop yields. Recently, we reported that a plastid‐targeting base editor named ptpTALECD, in which a cytidine deaminase DddA functions as the catalytic domain, can homoplasmically substitute a targeted C to T in plastid genomes of Arabidopsis thaliana. However, some target Cs were not substituted. In addition, although ptpTALECD could substitute Cs on the 3′ side of T and A, it was unclear whether it could also substitute Cs on the 3′ side of G and C. In this study, we identified the preferential positions of the substituted Cs in ptpTALECD‐targeting sequences in the Arabidopsis plastid genome. We also found that ptpTALECD could substitute Cs on the 3′ side of all four bases in plastid genomes of Arabidopsis. More recently, a base editor containing an improved version of DddA (DddA11) was reported to substitute Cs more efficiently, and to substitute Cs on the 3′ side of more varieties of bases in human mitochondrial genomes than a base editor containing DddA. Here, we also show that ptpTALECD_v2, in which a modified version of DddA11 functions as the catalytic domain, more frequently substituted Cs than ptpTALECD in the Arabidopsis plastid genome. We also found that ptpTALECD_v2 tended to substitute Cs at more positions than ptpTALECD. Our results reveal that ptpTALECD can cause a greater variety of codon changes and amino acid substitutions than previously thought, and that ptpTALECD and ptpTALECD_v2 are useful tools for the targeted base editing of plastid genomes. Significance Statement The preferred positions of cytosines that are substituted by a plastid‐targeted base editor, named ptpTALECD, were determined for more precise base editing in the Arabidopsis plastid genome. We also compared the substitution frequencies between ptpTALECD and the developed version of ptpTALECD (ptpTALECD_v2) and found that both ptpTALECD and ptpTALECD_v2 can be used to edit the plastid genome of Arabidopsis thaliana.
ISSN:0960-7412
1365-313X
DOI:10.1111/tpj.16311