PPR

Fujii S, Bond CS & Small ID 2011 Selection patterns on restorer-like genes reveal a conflict between nuclear and mitochondrial genomes throughout angiosperm evolution. PNAS, in press.
doi:10.1073/pnas.1007667108

  • most angiosperms for which extensive genomic sequence data exist contain multiple PPR genes related to Rf genes
  • these Rf-like genes show a number of characteristic features compared with other PPR genes, including chromosomal clustering and unique patterns of evolution, notably high rates of nonsynonymous to synonymous substitutions, suggesting diversifying selection
  • the highest probabilities of diversifying selection were seen for amino acid residues 1, 3, and 6 within the PPR motif
  • these residues are likely to form base-specific contacts to the RNA ligand
  • the selection patterns on Rf-like genes reveal a molecular "arms-race" between the nuclear and mitochondrial genomes that has persisted throughout most of the evolutionary history of angiosperms
  • each Rf gene prevents the expression of a single specific mitochondrial CMS gene
  • populations with polymorphic Rf alleles can display gynodioecy, where the population consists of a mixture of hermaphrodites and females
  • gynodioecy is fairly common in flowering plants (observed in about 7% of the species)
  • a key prediction of CMS theory is rapid fixation of both CMS genes and the corresponding Rf allele
  • most molecularly characterized CMS-Rf systems are in hermaphroditic taxa and are only revealed in wide crosses
  • thus, the importance of Rf evolution is much broader than its role in gynodioecy
  • new Rf alleles are expected to arise by mutations that alter target recognition
  • the clustering of RFL alleles ... promotes unequal crossovers and gene conversion
  • the linear, modular structure of PPR proteins (Fig. 5) implies that motif duplication, deletion, or exchange by recombination can all give rise to functional variants with altered target recognition
  • the expectation that Rf alleles evolve primarily by protein-coding changes as opposed to changes in expression levels or patterns must hold for the analysis of diversifying selection undertaken here to be informative
  • we are unaware of any reported observation of CMS in natural populations of A. thaliana