Interplay of endonucleolytic and exonucleolytic processing in the 3′-end formation of a mitochondrial nad2 RNA precursor in Arabidopsis

Abstract

Abstract Initiation and termination of plant mitochondrial transcription are poorly controlled steps. Precursor transcripts are thus often longer than necessary, and 3′-end processing as well as control of RNA stability are essential to produce mature mRNAs in plant mitochondria. Plant mitochondrial 3′ ends are determined by 3′-to-5′ exonucleolytic trimming until the progression of mitochondrial exonucleases along transcripts is stopped by stable RNA structures or RNA binding proteins. In this analysis, we investigated the function of the endonucleolytic mitochondrial stability factor 1 (EMS1) pentatricopeptide repeat (PPR) protein and showed that it is essential for the production and the stabilization of the mature form of the nad2 exons 1–2 precursor transcript, whose 3′ end corresponds to the 5′ half of the nad2 trans-intron 2. The accumulation of an extended rather than a truncated form of this transcript in ems1 mutant plants suggests that the role of EMS1 in 3′ end formation is not strictly limited to blocking the passage of 3′-5′ exonucleolytic activity, but that 3′ end formation of the nad2 exons 1–2 transcript involves an EMS1-dependent endonucleolytic cleavage. This study demonstrates that the formation of the 3′ end of mitochondrial transcripts may involve an interplay of endonucleolytic and exonucleolytic processing mediated by PPR proteins.