AtmtPNPase is required for multiple aspects of the 18S rRNA metabolism in Arabidopsis thaliana mitochondria

Plant mitochondria contain three rRNA genes, rrn26, rrn18 and rrn5, the latter two being co-transcribed. We have recently identified a polynucleotide phosphorylase-like protein (AtmtPNPase) in Arabidopsis mitochondria. Plants downregulated for AtmtPNPase expression (PNP− plants) accumulate 18S rRNA species polyadenylated at internal sites, indicating that AtmtPNPase is involved in 18S rRNA degradation. In addition, AtmtPNPase is required to degrade the leader sequence of 18S rRNA, a maturation by-product excised by an endonucleolytic cut 5′ to the 18S rRNA. PNP− plants also accumulate 18S rRNA precursors correctly processed at their 5′ end but containing the intergenic sequence (ITS) between the 18S and 5S rRNA. Interestingly, these precursors may be polyadenylated. Taken together, these results suggest that AtmtPNPase initiates the degradation of the ITS from 18S precursors following polyadenylation. To test this, we overexpressed in planta a second mitochondrial exoribonuclease, AtmtRNaseII, that degrades efficiently unstructured RNA including poly(A) tails. This resulted also in the detection of 18S rRNA precursors showing that AtmtRNaseII is not able to degrade the ITS but can impede the action of AtmtPNPase in initiating the degradation of the ITS. These results show that AtmtPNPase is essential for several aspects of 18S rRNA metabolism in Arabidopsis mitochondria.