Gene Families Required for Organelle RNA Editing

At least three plant gene families are required for chloroplast and/or mitochondrial C-to-U RNA editing, which is carried out by nuclear-encoded protein complexes.  Members of the large pentatricopeptide repeat (PPR)-containing protein family are site-specific recognition factors.  PPR proteins evidently bind to cis-elements immediately upstream of the C target of editing.  Similarity between different cis-elements permits recognition of multiple transcripts by a single PPR protein; for example, loss of a single PPR protein affects editing of 5 different chloroplast Cs.  Many PPR proteins are needed for recognition of the >600 Cs that are edited in Arabidopsis mitochondria. Immunoprecipitation of a PPR editing factor, followed by disruption of expression of candidate genes through mutation or silencing, identified members of the RIP (RNA editing factor-Interacting Protein) gene family as components of the RNA editing apparatus.  Individual RIP family members are required for editing of multiple C targets in either mitochondria or chloroplasts, or for editing in both organelles.  Sequence similarity between the RIP family and a protein containing an RNA recognition motif (RRM) resulted in the discovery that ORRM1 (Organelle RRM-containing protein) is required for editing of multiple chloroplast C targets.  ORRM1 is a member of a clade of genes in the Arabidopsis RRM-encoding gene family, thus implicating additional family members as candidate RNA editing factors.  Analysis of additional ORRM clade members is underway with the efficient STS-PCRseq method we developed for high-throughput analysis of editing extent.  Our goal is to identify the complete protein composition(s) of the plant organelle RNA editing apparatus.