Pentatricopeptide repeat proteins involved in plant organellar RNA editing

Abstract

C-to-U RNA editing has been widely observed in organellar RNAs in terrestrial plants. Recent research has revealed the significance of a large, plant-specific family of pentatricopeptide repeat (PPR) proteins for RNA editing and other RNA processing events in plant mitochondria and chloroplasts. PPR protein is a sequence-specific RNA-binding protein that identifies specific C residues for editing. Discovery of the RNA recognition code for PPR motifs, including verification and prediction of the individual RNA editing site and its corresponding PPR protein, expanded our understanding of the molecular function of PPR proteins in plant organellar RNA editing. Using this knowledge and the co-expression database, we have identified two new PPR proteins that mediate chloroplast RNA editing. Further, computational target assignment using the PPR RNA recognition codes suggests a distinct, unknown mode-of-action, by which PPR proteins serve a function beyond site recognition in RNA editing.

Tetrapyrrole biosynthetic enzyme protoporphyrinogen IX oxidase 1 is required for plastid RNA editing

“…The PLS subfamily of PPR proteins recognizes distinct targets for RNA editing (6)(7)(8)(9)(10)(11). A number of PPR factors, including CRR4, CRR28, OTP80, and OTP82, and a DYW domain-containing protein, DYW1, are known to be involved in the editing of ndhB and ndhD transcripts (22)(23)(24)(25)(26), which we show in this study to contain editing sites severely affected in ppo1.…”

“…The current consensus RNA editing model predicts that PPR proteins specifically recognize cis elements near the target cytidine residue and provide a platform for molecular attachment of other editing factors, such as MORF proteins (1,7,10,11,35). MORFs act as bridges that physically link PPR or related proteins to PPO1 through specific regions (Fig.…”

“…A series of studies identified members of the PLS subfamily of pentatricopeptide repeat (PPR) motif-containing proteins as the site-specific recognition factors for cytidine targets (6). These specific PPR trans-acting proteins recognize cis elements within a region of ∼30 nt within the sites to be edited (1,(6)(7)(8)(9)(10)(11). Although the DYW domains of some PPR factors contain several conserved residues with a cytidine deaminase motif (12), the enzyme that executes the editing reaction is elusive.…”

RNA Processing Factor 7 and Polynucleotide Phosphorylase Are Necessary for Processing and Stability of nad2 mRNA in Arabidopsis Mitochondria

“…3). Considering the nad2 transcript pattern in rpf7-1 and Chat-1, which both harbor RPF7 knockout alleles, and the nad2 RNA pattern in Can-0, we concluded that the latter accession also encodes a non-functional RPF7 gene, here caused by the presence of a premature translation stop codon within PPR motif P 6 . In summary these results strongly suggest that PPR motifs P 6 and P 7 are critical for RPF7 function in nad2 transcript maturation.…”

“…[1][2][3][4][5] In these organelles, PPR proteins specify cytidines to be converted to uridines by RNA editing. 6 PPR proteins involved in this process group into subclass PLS, according to their composition of canonical (P), short (S) and long (L) repeats. 7 PPR proteins are also involved in intron splicing as well as in 5′ and 3′ end formation of organellar transcripts.…”