Plant Spellcheckers: Molecular Basis of PPR-mediated RNA Editing and a Model for Retrograde Communication

RNA editing in plants converts cytidines to uridines (C-to-U) in chloroplast andmitochondrial transcripts. Pentatricopeptide repeat (PPR) protein family members havebeen shown to be required for editing, and possess key characteristics of editingdeaminases found in other organisms. PPRs have an N-terminal RNA binding domainresponsible for RNA recognition and a C-terminal DYW domain that has deaminase-likecharacteristics.The role of several features of the DYW domain was investigated. The DYW domainincludes the HXE motif that provides a glutamate residue that is catalytically required.Glutamate to alanine substitution ablated editing, and establishes a key characteristic ofthe DYW domain that is required for editing. In addition, a highly conserved PG box wasidentified between the N- and C-terminal domains that was required for editing in PPRsthat lacked a DYW domain, and the PG box may be required for protein-protein interactions to recruit a deaminase in trans. These observations led to the developmentof the cis and trans-editing models for RNA editing that posits that the deaminase may beprovided in cis from a single PPR or in trans in PPRs that lack a DYW domain. PPRs, such as MEF8, which have a short RNA binding domain and an intact deaminase domain,were identified as candidates for a trans-deaminases. RNAseq analysis was performedon mef8 null mutants and catalytically ablated variants to examine the role of MEF8 inmitochondrial editing. Sixty editing sites were affected, and suggests that MEF8 mayparticipate as a trans-editing deaminase by providing deaminase capability for a largenumber of editing sites.The role of reactive oxygen species (ROS) during editing dysfunction was investigated toexamine the potential mechanisms of sensing and signaling oxidative distress. LPA66mutant plants fail to edit a photosystem II polypeptide and exhibit a strong phenotype.Mutant plants produced elevated levels of ROS, and transcriptomic analysis revealedhigher expression of ROS reactive network genes and PPR or editing related genes.Lipidomics analysis of the mutant indicated highly elevated levels of oxylipins includingarabidoside A and G and phytoprostanes. Possible signaling mechanisms throughoxylipins and jasmonic acid pathways are discussed