Improved Computational Target Site Prediction for Pentatricopeptide Repeat RNA Editing Factors

Anja Zehrmann,Stefan Maas,Knut Graichen,Axel Brennicke,Mizuki Takenaka

doi:10.1371/journal.pone.0065343

Abstract

Pentatricopeptide repeat (PPR) proteins with an E domain have been identified as specific factors for C to U RNA editing in plant organelles. These PPR proteins bind to a unique sequence motif 5′ of their target editing sites. Recently, involvement of a combinatorial amino acid code in the P (normal length) and S type (short) PPR domains in sequence specific RNA binding was reported. PPR proteins involved in RNA editing, however, contain not only P and S motifs but also their long variants L (long) and L2 (long2) and the S2 (short2) motifs. We now find that inclusion of these motifs improves the prediction of RNA editing target sites. Previously overlooked RNA editing target sites are suggested from the PPR motif structures of known E-class PPR proteins and are experimentally verified. RNA editing target sites are assigned for the novel PPR protein MEF32 (mitochondrial editing factor 32) and are confirmed in the cDNA.

Highlights

The in plants vastly expanded family of pentatricopeptide repeat (PPR) proteins provides diverse RNA maturation functions mostly to the two organelles mitochondria and plastids [1,2]
Amino acid positions 6 and 19, respectively, in each PPR motif were noted to show correlations between amino acid identity and the presumably contacted nucleotide identity. These could function as discriminators to convey RNA sequence specificity depending on the order of the repeat elements in the respective PPR protein
The L, S2 and L2 type motifs were not considered as RNA binding elements but as spacers between P and S motifs

Summary

Introduction

The in plants vastly expanded family of pentatricopeptide repeat (PPR) proteins provides diverse RNA maturation functions mostly to the two organelles mitochondria and plastids [1,2]. All PPR proteins identified to be involved in RNA editing belong to this class [5]. Only one exception has been documented where a protein with only PPR repeats but no extension influences editing at several sites [6]. A number of PPR RNA editing proteins have been identified through analysis of mutants with phenotypic defects in organellar functions. Other analogous mutants do not show physiological phenotypes and require a direct comprehensive analysis of all editing sites. Since this is very labour and cost intensive for the more than 400 sites in mitochondria, a tool to predict target sites from the sequence of a given candidate PPR protein will be very useful

Methods

Results

Discussion

Conclusion