Elucidation of the RNA Recognition Code for Pentatricopeptide Repeat Proteins Involved in Organelle RNA Editing in Plants

Yusuke Yagi, Shimpei Hayashi, Keiko Kobayashi, Takashi Hirayama, Takahiro Nakamura

Research output: Contribution to journalArticle

142 Citations (Scopus)

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.

Original languageEnglish
Article numbere57286
JournalPLoS One
Volume8
Issue number3
DOIs
Publication statusPublished - Mar 5 2013

Fingerprint

RNA Editing
RNA editing
Organelles
organelles
RNA
Proteins
proteins
Amino Acids
amino acids
Nucleotides
nucleotides
RNA-binding proteins
RNA-Binding Proteins
Genes
Processing

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Elucidation of the RNA Recognition Code for Pentatricopeptide Repeat Proteins Involved in Organelle RNA Editing in Plants. / Yagi, Yusuke; Hayashi, Shimpei; Kobayashi, Keiko; Hirayama, Takashi; Nakamura, Takahiro.

In: PLoS One, Vol. 8, No. 3, e57286, 05.03.2013.

Research output: Contribution to journalArticle

Yagi, Yusuke ; Hayashi, Shimpei ; Kobayashi, Keiko ; Hirayama, Takashi ; Nakamura, Takahiro. / Elucidation of the RNA Recognition Code for Pentatricopeptide Repeat Proteins Involved in Organelle RNA Editing in Plants. In: PLoS One. 2013 ; Vol. 8, No. 3.
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