Targeted A-to-G base editing of chloroplast DNA in plants

Chloroplast DNA (cpDNA) encodes up to 315 (typically, 120-130) genes(1), including those for essential components in photosystems I and II and the large subunit of RuBisCo, which catalyses CO2 fixation in plants. Targeted mutagenesis in cpDNA will be broadly useful for studying the functions of these genes in molecular detail and for developing crops and other plants with desired traits. Unfortunately, CRISPR-Cas9 and CRISPR-derived base editors, which enable targeted genetic modifications in nuclear DNA, are not suitable for organellar DNA editing(2), owing to the difficulty of delivering guide RNA into organelles. CRISPR-free, protein-only base editors (including DddA-derived cytosine base editors(3-8) and zinc finger deaminases(9)), originally developed for mitochondrial DNA editing in mammalian cells, can be used for C-to-T, rather than A-to-G, editing in cpDNA(10-12). Here we show that heritable homoplasmic A-to-G edits can be induced in cpDNA, leading to phenotypic changes, using transcription activator-like effector-linked deaminases(13).

Automated summary

Chloroplast DNA encodes important genes, but current gene editing technologies cannot be used for editing organellar DNA. However, a new CRISPR-free, protein-only base editor can be used for C-to-T mutations in chloroplast DNA. We demonstrate the heritable A-to-G edits in chloroplast DNA, leading to phenotypic changes, by using transcription activator-like effector-linked deaminases.