Plant mitochondrial transcripts undergo maturation processes at both termini. Although frequently observed, the post-transcriptional formation of mature 5′ ends is still poorly understood. We now analyzed the processing of transcripts derived from the mitochondrialccmCgene, coding for a component of the cytochromecmaturation system. InArabidopsis thaliana(Arabidopsis) there are two mitochondrialccmCconfigurations, discriminated by a 66-bp sequence segment located approximately 500 bp upstream of theccmCgene. In Arabidopsis accessions these divergent mitochondrial genotypes correlate with the generation of two different 5′ termini that map to positions around −484 in accession Columbia (ColccmCgenotype) or −390 in accession C24 relative to the translation start codon (C24ccmCgenotype). Previously we identified RNA PROCESSING FACTOR 3 (RPF3), a pentatricopeptide repeat (PPR) protein required for the maturation ofccmCmRNAs with −484 5′ ends transcribed from the ColccmCgenotype. Now we identified several accessions defective in maturation ofccmCtranscripts. Taking advantage of this natural genetic variation we identified RNA PROCESSING FACTOR 6 (RPF6), a PPR protein necessary for the generation ofccmCmRNAs with −390 5′ ends transcribed from the C24ccmCgenotype. Both Col-type and C24-type accessions encode RPF3 and RPF6 so that they can processccmCtranscripts derived from the two different mitochondrial genotypes. These factors and their cognate RNA recognition sites in the differentccmCgenotypes are an intriguing example for the evolution of two co-adapted cyto-nuclear systems required for the same process i.e. 5′ maturation ofccmCtranscripts.Significance Statement
InArabidopsisaccessions two divergent mitochondrial genotypes correlate with the generation of ccmC mRNAs of distinct sizes. These transcripts have identical 3′ ends but differ at their 5′ termini. The previously characterized RNA PROCESSING FACTOR 3 is required for the maturation of ccmC mRNAs in Col genotype accessions. Now we identified RNA PROCESSING FACTOR 6 (RPF6), a PPR protein involved the formation of ccmC transcripts in C24 genotype accessions.