Maturase K forms a plastidial splicing complex with a neofunctionalized branching enzyme

Abstract Chloroplast group IIA introns originate from bacterial ribozymes. Their splicing requires the splicing factor Maturase K (MatK). MatK, however, has been difficult to functionally analyze, as it appears essential for plant viability and is encoded in the chloroplast genome. Here we identified a heteromultimeric complex comprising MatK and three other essential, plastid-targeted proteins using co-immunoprecipitation experiments in Arabidopsis and tobacco. Among the MatK interactors is a conserved homologue of starch-branching enzymes (BEs), which we named MATURASE K INTERACTING PROTEIN1 (MKIP1). We demonstrate that MKIP1 proteins have lost BE activity and acquired a 150-amino acid insertion that enables direct interaction with MatK’s N-terminus. Immunoprecipitation of Arabidopsis MKIP1 co-precipitates all known MatK intron targets. Inducing MKIP1 silencing in Arabidopsis causes newly emerging leaves to be pale, in which the splicing of MatK intron targets is strongly reduced. Our data suggest that MKIP1 functionally diverged from canonical BEs to facilitate splicing in conjunction with MatK. In turn, the former reverse-transcriptase domain in the N-terminal region of MatK likely has acquired the capacity to interact with other proteins. Potentially, complex formation allowed MatK to diversify its RNA interactions, helping its transition towards a general splicing factor.