Improved computational target site prediction for pentatricopeptide repeat RNA editing factors

PLoS One. 2013 Jun 6;8(6):e65343. doi: 10.1371/journal.pone.0065343. Print 2013.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Amino Acid Motifs
  • Arabidopsis / genetics*
  • Arabidopsis / metabolism
  • Arabidopsis Proteins / chemistry
  • Arabidopsis Proteins / genetics*
  • Arabidopsis Proteins / metabolism
  • Base Sequence
  • Computer Simulation
  • Gene Expression Regulation, Plant*
  • Molecular Sequence Data
  • Protein Isoforms / chemistry
  • Protein Isoforms / genetics
  • Protein Isoforms / metabolism
  • RNA Editing*
  • RNA-Binding Proteins / chemistry
  • RNA-Binding Proteins / genetics*
  • RNA-Binding Proteins / metabolism

Substances

  • Arabidopsis Proteins
  • Protein Isoforms
  • RNA-Binding Proteins
  • pentatricopeptide repeat protein, Arabidopsis

Grant support

This work was supported by grants TA624/2-2, TA624/3-1, TA624/4-1 and BR726/11-1 from the DFG (www.dfg.de). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.