MEF46 and MEF47 are novel specificity factors for RNA editing sites in mitochondrial nad transcripts.

• In silico prediction identified target RNA editing sites of two PPR proteins. • MEF46 is an E+ subclass PPR and required for RNA editing at nad5 -1958. • MEF47 is an E subclass PPR and essential for two sites, nad3 -64 and ccmC -614. • The target of MEF46 is a target of DYW2 as well, while those of MEF47 are not. • These results support the functional connection between E+ subclass PPRs and DYW2. Terrestrial plants have C-to-U RNA editing in the transcripts of plastids and mitochondria. Target specificity for more than several hundred editing sites are governed by PLS (P PR, L ong and S hort) class Pentatricopeptide repeat (PPR) proteins with additional C-terminal domains. Half of these PPR proteins have DYW (Aspartate (D), Tyrosine (Y) and Tryptophan (W)) domains, which most likely harbour cytidine deaminase activity. The other half of them, E subclass and E+ subclass proteins, contain no or only a part of the DYW domain. Missing DYW domains in the E and E+ subclass PPR proteins are likely to be complemented by other DYW containing proteins. All target sites of so far characterized E+ subclass PPR proteins show defects in dyw2 mutants, suggesting that the DYW2 protein complements the missing DYW domains in the E+ subclass PPR proteins. Here we report two novel RNA editing factors, MEF46 and MEF47, which belong to E+ and E subclass, respectively. The defective editing site in mef46, nad5 -1958 , overlaps with the affected sites in dyw2 mutants, while that in mef47 , nad3 -64 and ccmC -614 do not, further supporting the specific functional connection between E+ subclass PPR proteins and DYW2. [ABSTRACT FROM AUTHOR]