PPR

Nakamura T, Yagi Y & Kobayashi K 2012 Mechanistic insight into pentatricopeptide repeat proteins as sequence-specific RNA-binding proteins for organellar RNAs in plants. Plant Cell Physiol 53:1171-1179.

  • the phenotypes of PPR mutants are highly diverse
  • their impacts are often severe
  • the disruption of a single PPR gene, in many cases, has resulted in embryonic lethality, presumably because of the impairment of mitochondrial function
  • the consecutive helical hairpins in a PPR tract are predicted to form a curved structure resembling half a donut or crescent
  • this structure is similar to those found in the helical repeat protein family, such as the TPR motif (34 amino acids), HEAT domain (39 amino acids), Arm motif (38 amino acids) and Puf domain (36 amino acids)
  • the HEAT, Arm and TPR motifs are responsible for protein–protein interactions
  • the concave surface of the crescent is the interaction site
  • the Puf domain uses the same surface for RNA binding
  • the PPR motif was originally identified as a 35 amino acid motif and was later subdivided into the P (classical PPR; 35 amino acids), PPR-like S (short; 31 amino acids), PPR-like L1 (long; 35 amino acids) and L2 (36 amino acids) motifs based on their sequence characteristics
  • the limitation of structural and functional knowledge about PPR motifs and the mechanism by which they contact RNA makes it challenging to define the functionality of PPR motifs accurately
  • the five residues [first, fourth, eighth, 12th and 'ii' (−2) amino acids] exposed on the solvent surface seem to organize the RNA-binding surface
  • the editing PPR proteins generally distinguish pyrimidines from purines, and, at some positions, recognize specific bases
  • the PPR protein has been hypothesized to interact with RNA in a sequence-specific manner via one-motif to one-nucleotide correspondence
  • participation of an additional, unexpected class of protein, multiple organellar RNA-editing factor (MORF), has been identified for RNA editing machinery in plant organelles
  • proteins in this family require efficient RNA editing of multiple, or even dozens, of sites via physical interaction with PPR proteins
  • the species-specific PPR proteins are homologous to the product of Rf genes found in several species
  • these Rf-like PPR genes show a number of characteristic features compared with other PPR genes, including chromosomal clustering, unique patterns of evolution and high rates of diversifying selection
  • why have plants alone acquired so many PPR genes
  • why are proteins with this motif exclusively involved in symbiotic organelle gene expression across organisms