PPR

O'Toole N, Hattori M, Andres C, Iida K, Lurin C, Schmitz-Linneweber C, Sugita M & Small I 2008 On the expansion of the pentatricopeptide repeat gene family in plants. Mol Biol Evol 25:1120-1128.

• a large majority of the PPR genes in each of the flowering plants are intron less
• most of the 103 PPR genes in Physcomitrella are intron rich
• one or more waves of retrotransposition were responsible for the expansion of the PPR gene family in flowering plants
• the differing numbers of PPR proteins are highly correlated with differences in organellar RNA editing between the 3 species

• the complete nuclear genome of A. thaliana contains 450 distinct genes encoding PPR proteins, separated into 2 subfamilies and 4 subclasses based on their C-terminal domain structure

• PPR genes can be divided into 4 subclasses based on their C-terminal domain structure and the presence of longer (L) or shorter (S) variant PPR motifs within the tandem arrays of the classic P PPR
• a large majority of moss PPR proteins belong to the P subclass, apart from a small set of DYW subclass proteins
• no E subclass PPR genes are found in moss, compared with over 100 in Arabidopsis and rice
• note the similar number of genes in Arabidopsis and rice in the various PPR subclasses

• in eukaryotes that are intron poor, introns are preferentially located at the 5' ends of genes

• 2 regions of the phylogenetic tree in figure 3A do not conform to the general trend observed above and consist of groups of rice-specific and Arabidopsis-specific paralogs
• these proteins in these regions are homologous to the restorer-of-fertility (Rf) genes
• these genes cluster in chromosomes 1 and 10 of Arabidopsis and rice, respectively
• recently (Geddy and Brown 2007) have demonstrated that radish Rf genes have been subject to diversifying selection
• the unusual evolutionary relationships of Rf genes and their functional implications will be treated elsewhere