Elucidation of the RNA recognition code for pentatricopeptide repeat proteins involved in organelle RNA editing in plants

PLoS One. 2013;8(3):e57286. doi: 10.1371/journal.pone.0057286. Epub 2013 Mar 5.

Abstract

Pentatricopeptide repeat (PPR) proteins are eukaryotic RNA-binding proteins that are commonly found in plants. Organelle transcript processing and stability are mediated by PPR proteins in a gene-specific manner through recognition by tandem arrays of degenerate 35-amino-acid repeating units, the PPR motifs. However, the sequence-specific RNA recognition mechanism of the PPR protein remains largely unknown. Here, we show the principle underlying RNA recognition for PPR proteins involved in RNA editing. The distance between the PPR-RNA alignment and the editable C was shown to be conserved. Amino acid variation at 3 particular positions within the motif determined recognition of a specific RNA in a programmable manner, with a 1-motif to 1-nucleotide correspondence, with no gap sequence. Data from the decoded nucleotide frequencies for these 3 amino acids were used to assign accurate interacting sites to several PPR proteins for RNA editing and to predict the target site for an uncharacterized PPR protein.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Amino Acids / metabolism
  • Arabidopsis / genetics
  • Arabidopsis / metabolism
  • Arabidopsis Proteins / genetics*
  • Bryopsida / genetics
  • Bryopsida / metabolism
  • Chloroplasts / metabolism
  • Genome, Plant
  • Mitochondria / metabolism
  • Nucleotides / metabolism
  • Organelles / metabolism*
  • RNA Editing*
  • RNA, Plant / metabolism*
  • RNA-Binding Proteins / metabolism*

Substances

  • Amino Acids
  • Arabidopsis Proteins
  • Nucleotides
  • RNA, Plant
  • RNA-Binding Proteins
  • pentatricopeptide repeat protein, Arabidopsis

Grant support

This work was supported by the Program for Basic and Applied Researches for Innovations in Bio-oriented Industry (BRAIN) from the Bio-oriented Technology Research Advancement Institution (T.N.; http://www.naro.affrc.go.jp/english/index.html); the Kyushu University Research Superstar Program (T.N.; http://www.srp.kyushu-u.ac.jp/ssp_home/e_top.html) from Kyushu University; and Grants-in-Aid 22681028 and 22380008 (T.N.) and 20570050, 21112521, and 23112715 (T.H.) from the Ministry of Education, Culture, Sports, Science, and Technology (http://www.jsps.go.jp/english/index.html). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.