DYW deaminase domain has a distinct preference for neighboring nucleotides of the target RNA editing sites

• Published in: The Plant journal : for cell and molecular biology 2022-08, Vol.111 (3), p.756-767
• Main Authors: Maeda, Ayako, Takenaka, Sachi, Wang, Tenghua, Frink, Brody, Shikanai, Toshiharu, Takenaka, Mizuki
• Format: Article
• Language: English
• Subjects: Bias; chloroplast; Deamination; Domains; DYW domain; E coli; Editing; mitochondria; Nucleotide sequence; Nucleotides; Organelles; pentatricopeptide repeat proteins; RNA editing
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/tpj.15850

SUMMARY C‐to‐U RNA editing sites in plant organelles show a strong bias for neighboring nucleotides. The nucleotide upstream of the target cytidine is typically C or U, whereas A and G are less common and rare, respectively. In pentatricopeptide repeat (PPR)‐type RNA editing factors, the PPR domain specifically binds to the 5′ sequence of target cytidines, whereas the DYW domain catalyzes the C‐to‐U deamination. We comprehensively analyzed the effects of neighboring nucleotides of the target cytidines using an Escherichia coli orthogonal system. Physcomitrium PPR56 efficiently edited target cytidines when the nucleotide upstream was U or C, whereas it barely edited when the position was G or the nucleotide downstream was C. This preference pattern, which corresponds well with the observed nucleotide bias for neighboring nucleotides in plant organelles, was altered when the DYW domain of OTP86 or DYW1 was adopted. The PPR56 chimeric proteins edited the target sites even when the −1 position was G. Our results suggest that the DYW domain possesses a distinct preference for the neighboring nucleotides of the target sites, thus contributing to target selection in addition to the existing selection determined by the PPR domain. Significance Statement In C‐to‐U RNA editing of plant organelles, the pentatricopeptide repeat (PPR) domain specifically recognizes the 5′ sequence of the target cytidines, whereas the DYW domain catalyzes C‐to‐U deamination. We demonstrated that the DYW domain shows a distinct preference for the neighboring nucleotides of the target site using an orthogonal bacterial editing assay system. Our findings suggest that the DYW domain and the PPR domain coordinate to specify target RNA editing sites in plant organelles.