PPR type RNA editing factors

PPR proteins

More than 50 PPR proteins (pentatricopeptide repeat) have been identified as site-specific trans-factors of RNA editing in plant mitochondria and plastids. In our lab, we have found more than twenty PPR type RNA editing factors involved in mitochondria that we named MEF (mitochondrial RNA editing factor) proteins.

PPR proteins involved in RNA editing are characterized by a varying number of repeated elements with loose similarity. The PPR domain can be made up of 35 (P-elements), 31 (S for small) or 36 (L for large) amino acids. Additionally, all of these factors contain a C-terminal extension (E domain) and some also another domain, which canonically terminates with the tripeptide Aspartate (D), Tyrosine (Y), and Tryptophan(W) (DYW domain )(Fig. 1). Most of these trans-factors are required for editing to occur at one or more sites, some (e.g. MEF8, MEF8S, DYW2) act as cofactors which enhance editing levels at one or more sites.

Each PPR motif recognizes a nucleotide with sequence specific manner, thus PPR type editing factors can distinguish distinct RNA editing sites. DYW domain has two Zinc binding motif which are typically observed in cytidine deaminases, suggesting the domain confers enzymatic activity for C to U editing reaction. Recently reported introduction of C to U editing in E.coli as well as in vitro RNA editing by a single DYW containing PPR protein, supporting the hypothesis. Crystal strucutures of the DYW domain suggested an unusual regulation of the DYW cytidine deaminase.