PPR

Hernandez Mora JR, Rivals E, Mireau H & Budar F 2010 Sequence analysis of two alleles reveals that intra-and intergenic recombination played a role in the evolution of the radish fertility restorer (Rfo). BMC Plant Biol 10:35.

  • some PPR proteins were shown to participate in post-transcriptional events involved in organellar gene expression
  • this type of function is now thought to be their main biological role
  • we sequenced a non-restoring allele (L7rfo) of the Rfo radish locus whose restoring allele (D81Rfo) was previously described
  • the L7rfo allele carries two genes (PPR-1 and PPR-2) closely related to the three previously described PPR genes of the restorer D81Rfo allele (PPR-A, PPR-B, and PPR-C)
  • the Rfo locus appears to experience more complex evolution than its flanking sequences
  • the Rfo locus and PPR genes therein are likely to evolve as a result of intergenic and intragenic recombination
  • it is therefore not possible to determine which genes on the two alleles are direct orthologs
  • Rf genes are carried on complex loci, containing several closely related genes, generally unable to restore fertility
  • the restoring allele of the radish Rfo locus, here named D81Rfo, carries three related PPR genes arbitrarily named PPR-A, PPR-B, and PPR-C
  • the PPR-B gene confers the fertility restoration activity, whereas PPR-A and PPR-C do not
  • PPR-C was shown to be a pseudogene
  • this led to the idea that Rf genes, unlike other PPR genes, might undergo an evolutionary process recalling that of resistance genes in plants
  • we describe the sequence and genetic organization of a non-restoring allele of the Rfo locus (L7rfo), isolated from a European radish cultivar that was selected for the absence of restorers
  • by comparing it with the previously described restorer allele (D81Rfo), originating from an Asian genotype
  • we describe two new PPR genes that are closely related to PPR-A, PPR-B, and PPR-C and investigate their phylogenetic relationship
  • these five related PPR genes share a common sequence organization, probably present in their common ancestor
  • we constructed a BAC library from the L7 radish line, which was selected from European radish cultivars for maintaining Ogura sterility
  • genomic clones carrying the L7rfo allele were selected using two PCR markers closely linked to the Rfo locus and previously identified during identification of the restorer allele (D81Rfo)
  • two regions of L7rfo showed 90 to 94% identity with the region of D81Rfo carrying the PPR genes
  • two PPR genes, named PPR-1 and PPR-2, were predicted
  • RT-PCR analyses indicated that both PPR-1 and PPR-2 are transcribed, at least in flower buds
  • sequencing of amplification products confirmed the presence of an intron in their 3' regions, as in PPR-A and PPR-B
  • like the D81Rfo PPR genes, PPR-1 and PPR-2 are predicted to encode proteins containing 17 PPR-P repeats
  • the putative PPR-1 and PPR-2 proteins contain the same four amino acid deletion in the third PPR repeat also found in PPR-A
  • the putative PPR-1 and PPR-2 proteins are transported to mitochondria
  • although the PPR-1 and PPR-2 genes are from a European radish cultivar, they group with PPR-A and PPR-C, respectively, which were sequenced from an Asian radish genotype
  • a PPR gene duplication at the Rfo locus predates the divergence of Asian and European genotypes
  • PPR-1 and PPR-A, on one hand, and PPR-2 and PPR-C, on the other hand, probably derived from two distinct copies of the Rfo PPR gene in the common ancestor of these two geographically isolated radish genotypes
  • a multiple alignment of gene sequences (Additional File 1) revealed polymorphisms shared between PPR-1 or PPR-2 and the genes from the D81Rfo sequence
  • we considered that a polymorphism was shared between two sequences when the nucleotide at this position was identical between the two considered sequences and different from that present at the same position in the three other genes
  • different parts of PPR-1 and PPR-2 share a most recent common ancestor with different genes of the D81Rfo allele
  • which implies that intragenic recombination occurred during gene evolution
  • the Ogura CMS system does not exist in any other species than wild and cultivated radishes (H. Yamagishi, personal communication)
  • the Ogura restoring function of PPR-B was selected in the radish lineage probably by duplication and neofunctionalization of a previously existing PPR gene, with a 17 repeat structure
  • it would therefore be particularly interesting to investigate what was the biological function of the PPR-B ancestor gene in a species were no Ogura CMS gene operated
  • an internal duplication, as those hypothesized in the evolution of some resistance genes [52,53], seems to be involved in the formation of Rfo-PPR genes