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Base editing of organellar DNA with programmable deaminases

Nature Reviews Molecular Cell Biology volume 25, pages 34–45 (2024)Cite this article

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Abstract

Mitochondria and chloroplasts are organelles that include their own genomes, which encode key genes for ATP production and carbon dioxide fixation, respectively. Mutations in mitochondrial DNA can cause diverse genetic disorders and are also linked to ageing and age-related diseases, including cancer. Targeted editing of organellar DNA should be useful for studying organellar genes and developing novel therapeutics, but it has been hindered by lack of efficient tools in living cells. Recently, CRISPR-free, protein-only base editors, such as double-stranded DNA deaminase toxin A-derived cytosine base editors (DdCBEs) and adenine base editors (ABEs), have been developed, which enable targeted organellar DNA editing in human cell lines, animals and plants. In this Review, we present programmable deaminases developed for base editing of organellar DNA in vitro and discuss mitochondrial DNA editing in animals, and plastid genome (plastome) editing in plants. We also discuss precision and efficiency limitations of these tools and propose improvements for therapeutic, agricultural and environmental applications.

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Fig. 1: The carbon cycle mediated by mitochondria and chloroplasts.
Fig. 2: The development of mitochondrial DNA base editors.
Fig. 3: Mitochondrial base editing in animals.
Fig. 4: Off-target mutations induced by mitochondrial base editors and strategies to reduce their frequency.
Fig. 5: Organellar DNA editing in plants.

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Acknowledgements

The authors thank W. Han and Y. Geun Mok for preparing the figures. This work was supported by grant 2018YFA0801401 (to J.C.) from the Ministry of Science and Technology, NK2022010207 (to J.C.) from the Ministry of Agriculture and Rural Affairs and a Shanghai Municipal Education Commission (SMEC) grant to the Shanghai Frontiers Science Center for Biomacromolecules and Precision Medicine at the ShanghaiTech University. J.-S.K. is supported by NUS Medicine Synthetic Biology Translational Research Program (NUHSRO/2020/077/MSC/02/SB) and the National Research Foundation of Korea (RS-2023-00260462).

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Authors and Affiliations

  1. NUS Synthetic Biology for Clinical & Technological Innovation (SynCTI) and Department of Biochemistry, National University of Singapore, Singapore, Singapore

    Jin-Soo Kim

  2. Edgene, Seoul, South Korea

    Jin-Soo Kim

  3. Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China

    Jia Chen

  4. Shanghai Clinical Research and Trial Center, Shanghai, China

    Jia Chen

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Both authors contributed equally to all aspects of the article.

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Correspondence to Jin-Soo Kim or Jia Chen.

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Competing interests

J.C. is a scientific co-founder and adviser of CorrectSequence Therapeutics, a company that uses gene-editing technologies. J.-S.K is a founder and shareholder of ToolGen, Edgene. and GreenGene, which are focused on genome editing.

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Nature Reviews Molecular Cell Biology thanks Shin-Ichi Arimura and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Related links

Mitomap: www.mitomap.org

Glossary

Bystander editing

Refers to the formation of unintended mutations in the editing window of a base editor.

Chloroplast transit peptide

(CTP). An N-terminal portion in a nuclear-encoded protein that directs the transport of the protein into chloroplasts. The CTP is cleaved off during the transport by a peptidase.

Interbacterial toxin

A toxin secreted from a bacterium that inhibits growth of competing bacteria.

Mitochondrial targeting sequence

(MTS). A peptide of 15–70 amino acids at the N terminus of a nuclear-encoded protein, which facilitates transport of the protein into mitochondria. The MTS is cleaved off during the transport by a peptidase.

Nickase

An enzyme that cleaves one strand of double-stranded DNA to produce a single-strand break (nick).

Phage-assisted evolution

A directed evolution methodology for protein engineering that exploits the phage life cycle in bacteria.

R-loop

A DNA–RNA hybrid structure consisting of a DNA strand hybridized with an RNA and a displaced DNA strand.

TALE arrays

Transcription activator-like effector (TALE) arrays bind to a target DNA sequence. The arrays are composed of highly homologous repeats of 34 amino acids, derived from the bacterial genus Xanthomonas.

Transfer DNA

(T-DNA). A DNA segment in a tumour-inducing plasmid, derived from agrobacterium, that is transferred to the genome of a host plant.

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Kim, JS., Chen, J. Base editing of organellar DNA with programmable deaminases. Nat Rev Mol Cell Biol 25, 34–45 (2024). https://doi.org/10.1038/s41580-023-00663-2

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