Redefining the Structural Motifs that Determine RNA Binding and RNA Editing by Pentatricopeptide Repeat Proteins in Land Plants

The nucleus-encoded pentatricopeptide repeat (PPR) proteins form one of the largest protein families in land plants. They are characterized by tandem 30-40 amino acid motifs that form an extended binding surface capable of sequence- specific recognition of RNA strands. Almost all of them are post-translationally targeted to plastids and mitochondria where they play important roles in post- transcriptional processes including splicing, RNA editing and the initiation of translation. A code describing how PPR proteins recognise their RNA targets promises to accelerate research on these proteins, but making use of this code requires accurate definition and annotation of all of the various nucleotide- binding motifs in each protein. We have used a structural modelling approach to define 10 different variants of the PPR motif found in plant proteins, in addition to the putative deaminase motif that is found at the C-terminus of many RNA editing factors. We have developed detailed structural models of each set of motif combinations commonly found in plant proteins. We show that the super- helical RNA binding surface of RNA editing factors is potentially longer than previously recognised. We used the redefined motifs to develop accurate and consistent annotations of PPR genes/proteins from 111 genomes/proteomes, providing a rich repository of PPR sequence datasets. We have been extending our researches of PPRs to the model fern genome (Azolla) and the 1000 transcriptome dataset (1kp project), to provide more comprehensive insights into this amazing gene family.